Schema for TOGA vs. hg38 - TOGA annotations using human/hg38 as reference
  Database: mm39    Primary Table: HLTOGAannotvHg38v1 Data last updated: 2022-06-20
Big Bed File Download: /gbdb/mm39/TOGAvHg38v1/HLTOGAannotVsHg38v1.bb
Item Count: 55,658
The data is stored in the binary BigBed format.

Format description: TOGA predicted gene model
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart129358567Start position in chromosome
chromEnd130145917End position in chromosome
nameENST00000272643.THSD7B.118Name or ID of item, ideally both human readable and unique
score1000Score (0-1000)
strand++ or - for strand
thickStart129358567Start of where display should be thick (start codon)
thickEnd130145917End of where display should be thick (stop codon)
itemRgb0,0,200RGB value (use R,G,B string in input file)
blockCount27Number of blocks
blockSizes139,811,249,170,156,198,192,235,116,130,104,195,267,180,139,151,142,116,118,146,160,174,96,83,193,88,82,Comma separated list of block sizes
chromStarts0,164539,182279,198046,236983,247218,327615,329438,345462,385812,391761,484722,490417,520559,672235,685729,728743,731989,734218,749521,757629,759025,759300,761723,764276,779410,787268,Start positions relative to chromStart
ref_trans_idENST00000272643.THSD7BReference transcript ID
ref_regionchr2:136882178-137677717Transcript region in the reference
query_regionchr1:129358567-130145917Region in the query
chain_score0.9963686466217041Chain orthology probability score
chain_synteny88Chain synteny log10 value
chain_flank0.4359Chain flank feature
chain_gl_cds_fract0.019213109051408092Chain global CDS fraction value
chain_loc_cds_fract0.012452949932794832Chain local CDS fraction value
chain_exon_cov1.0Chain exon coverage value
chain_intron_cov0.4847922998986829Chain intron coverage value
statusIntactGene loss classification
perc_intact_ign_M1.0% intact ignoring missing
perc_intact_int_M1.0% intact considering missing as intact
intact_codon_prop1.0% intact codons
ouf_prop0.0% out of chain
mid_intact1Is middle 80% intact
mid_pres1Is middle 80% fully present
prot_alignmentref: MFPKSNLTVTCWVWRSMRKLFLLLSLLLSHAAHLEGKKDNQFIWKPGPWGRCTGDCGPGGVQSRAVWCFHVDGWTSHLSN
     ||  | | || || |||||||| |||||| |||||| ||||| || |||||| ||||||| |||||||||  ||||  ||
que: MFLRSDLAVTHWVSRSMRKLFLVLSLLLSQAAHLEGRKDNQFLWKTGPWGRCAGDCGPGGAQSRAVWCFHIEGWTSPMSN

ref: CGESNRPPKERSCFRVCDWHSDLFQWEVSDWHHCVLVPYARGEVKPRTAECVTAQHGLQHRMVRCIQKLNRTVVANEICE
     | ||  |||||||||||||||||||||||||| | ||| | ||  ||  |||||||||||| ||| |||||| | |||||
que: CDESSQPPKERSCFRVCDWHSDLFQWEVSDWHRCLLVPGAQGEPRPRAVECVTAQHGLQHRTVRCLQKLNRTMVSNEICE

ref: HFALQPPTEQACLIPCPRDCVVSEFLPWSNCSKGCGKKLQHRTRAVIAPPLFGGLQCPNLTESRACDAPISCPLGEEEYT
     ||| ||||||||||||||||||||| ||| |  |||||||||||  ||||| |||||||||||||| || ||||| ||| 
que: HFAPQPPTEQACLIPCPRDCVVSEFSPWSTCPEGCGKKLQHRTRVAIAPPLYGGLQCPNLTESRACEAPVSCPLGKEEYS

ref: FSLKVGPWSKCRLPHLKEINPSGRTVLDFNSDSNERVTFKHQSYKAHHHSKSWAIEIGYQTRQVSCTRSDGQNAMLSLCL
     ||||||||||||||||||   |||   || ||||| ||  ||||||||||      || ||||| |||||| || |||| 
que: FSLKVGPWSKCRLPHLKEVDLSGRNIQDFSSDSNEQVTLTHQSYKAHHHSQPGDVVIGFQTRQVWCTRSDGRNALLSLCV

ref: QDSFPLTVQSCIMPKDCETSQWSSWSPCSKTCRSGSLLPGFRSRSRNVKHMAIGGGKECPELLEKEACIVEGELLQQCPR
      |||||||| | |||||||| || ||||||||||| | || ||||||||| ||||| ||||||||| || ||| || |||
que: RDSFPLTVQPCVMPKDCETSEWSPWSPCSKTCRSGTLSPGVRSRSRNVKHIAIGGGQECPELLEKETCIAEGEFLQPCPR

ref: YSWRTSEWKECQVSLLLEQQDPHWHVTGPVCGGGIQTREVYCAQSVPAAAALRAKEVSRPVEKALCVGPAPLPSQLCNIP
     ||||||||||||||||||| || || ||| ||||||||||||||| ||  | | ||||||||  || ||||  ||||| |
que: YSWRTSEWKECQVSLLLEQHDPLWHETGPICGGGIQTREVYCAQSLPATIASRTKEVSRPVERTLCLGPAPSASQLCNVP

ref: CSTDCIVSSWSAWGLCIHENCHDPQGKKGFRTRQRHVLMESTGPAGHCPHLVESVPCEDPMCYRWLASEGICFPDHGKCG
     || |||||||| || |  ||||||||||||| |||||||||||| | |||| |||||||||| |||||||||  ||||||
que: CSMDCIVSSWSTWGPCVFENCHDPQGKKGFRMRQRHVLMESTGPMGRCPHLAESVPCEDPMCHRWLASEGICIADHGKCG

ref: LGHRILKAVCQNDRGEDVSGSLCPVPPPPERKSCEIPCRMDCVLSEWTEWSSCSQSCSNKNSDGKQTRSRTILALAGEGG
     |||||||||||| ||| ||| ||||||||||  |||||||||| |||| ||||||||||||||||||||| |||||||||
que: LGHRILKAVCQNERGEEVSGGLCPVPPPPERMACEIPCRMDCVVSEWTVWSSCSQSCSNKNSDGKQTRSRSILALAGEGG

ref: KPCPPSQALQEHRLCNDHSCMQLHWETSPWGPCSEDTLVTALNATIGWNGEATCGVGIQTRRVFCVKSHVGQVMTKRCPD
     | || || ||| |||||||| || |||| || ||| ||||||| ||||||||||||||||| ||| ||||||||||||| 
que: KTCPSSQELQEYRLCNDHSCTQLYWETSAWGSCSENTLVTALNVTIGWNGEATCGVGIQTRKVFCIKSHVGQVMTKRCPE

ref: STRPETVRPCFLPCKKDCIVTAFSEWTPCPRMCQAGNATVKQSRYRIIIQEAANGGQECPDTLYEERECEDVSLCPVYRW
     |||||||||||||||||| |||||||||||| || || | ||||||||||||||||||||||| ||||||| |||| |||
que: STRPETVRPCFLPCKKDCLVTAFSEWTPCPRPCQPGNTTIKQSRYRIIIQEAANGGQECPDTLFEERECEDISLCPSYRW

ref: KPQKWSPCILVPESVWQGITGSSEACGKGLQTRAVSCISDDNRSAEMMECLKQTNGMPLLVQECTVPCREDCTFTAWSKF
     |||||| |||||||  || || |||||||||||||||||||| |||| ||||| |||| |||||| ||| ||||| ||||
que: KPQKWSSCILVPESIRQGRTGTSEACGKGLQTRAVSCISDDNQSAEMTECLKQMNGMPPLVQECTIPCRDDCTFTPWSKF

ref: TPCSTNCEATKSRRRQLTGKSRKKEKCQDSDLYPLVETELCPCDEFISQPYGNWSDCILPEGRREPHRG-LRVQADSKEC
     |||| |||||  |||||||||||||||||  |||||| | |||| | | |||||| |||||| |    | | || | |||
que: TPCSKNCEATQIRRRQLTGKSRKKEKCQDASLYPLVEMEPCPCDTFMSHPYGNWSACILPEGKRDAQQGGLWVQGDDKEC

ref: GEGLRFRAVACSDKNGRPVDPSFCSSSGYIQEKCVIPCPFDCKLSDWSSWGSCSSSCGIGVRIRSKWLKEKPYNGGRPCP
     ||| |||| |||  |||||||||| ||||||| |||||||||||||||||||||||||||||||||||||||| ||||||
que: GEGVRFRAIACSNINGRPVDPSFCNSSGYIQEACVIPCPFDCKLSDWSSWGSCSSSCGIGVRIRSKWLKEKPYSGGRPCP

ref: KLDLKNQGQVHEAVPCYSECNQYSWVVEHWSSCKINNELRSLRCGGGTQSRKIRCVNTADGEGGAVDSNLCNQDEIPPET
     ||||||| |||||||||||| |||||||||| ||||||||| ||| ||||| |||| ||| |||||   |||||  | ||
que: KLDLKNQVQVHEAVPCYSECDQYSWVVEHWSPCKINNELRSPRCGRGTQSRRIRCVSTADREGGAVNRSLCNQDDAPQET

ref: QSCSLMCPNECVMSEWGLWSKCPQSCDPHTMQRRTRHLLRPSLNSRTCAEDSQVQPCLLNENCFQFQYNLTEWSTCQLSE
     | ||| || |||||||| || |||||||| |||||||||||||||||| ||||| |||||||||||||||||||||||||
que: QACSLLCPSECVMSEWGTWSRCPQSCDPHAMQRRTRHLLRPSLNSRTCGEDSQVRPCLLNENCFQFQYNLTEWSTCQLSE

ref: NAPCGQGVRTRLLSCVCSDGKPVSMDQCEQHNLEKPQRMSIPCLVECVVNCQLSGWTAWTECSQTCGHGGRMSRTRFIIM
     |  ||||||||||||| |||| |||| ||| |||||||||||||||||||||||||| ||||||||| ||||||||||||
que: NVSCGQGVRTRLLSCVRSDGKSVSMDHCEQRNLEKPQRMSIPCLVECVVNCQLSGWTTWTECSQTCGQGGRMSRTRFIIM

ref: PTQGEGRPCPTELTQEKTCPVTPCYSWVLGNWSACKLEGGDCGEGVQIRSLSCMVHSGSISHAAGRVEDALCGEMPFQDS
     ||||||| ||||||| | ||||||||||||||||||||||||||||| || || || ||||| |  || ||||| |||  
que: PTQGEGRQCPTELTQQKPCPVTPCYSWVLGNWSACKLEGGDCGEGVQVRSFSCVVHNGSISHTAVPVEEALCGEVPFQEG

ref: ILKQLCSVPCPGDCHLTEWSEWSTCELTCIDGRSFETVGRQSRSRTFIIQSFENQDSCPQQVLETRPCTGGKCYHYTWKA
     ||||||||||||||| | ||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||| |||
que: ILKQLCSVPCPGDCHITPWSEWSKCELTCIDGRSFETTGRQSRSRTFIIQSFENQDSCPQQVLETRPCTGGKCYHYIWKA

ref: SLWNNNERTVWCQRSDGVNVTGGCSPQARPAAIRQCIPACRKPFSYCTQGGVCGCEKGYTEIMKSNGFLDYCMKVPGSED
     ||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||| | ||||||||||||||
que: SLWNNNERTVWCQRSDGLNVTGGCSPQARPAAIRQCIPACKKPFSYCTQGGVCGCEKGYTEIMRSSGFLDYCMKVPGSED

ref: KKADVKNLSGKNRPVNSKIHDIFKGWSLQPLDPDGRVKIWVYGVSGGAFLIMIFLIFTSYLVCKKPKPHQSTPPQQKPLT
     |||||||||||||||||||||||||||||||||||||| |||||||| ||||||| |||||||||||||||||  |||||
que: KKADVKNLSGKNRPVNSKIHDIFKGWSLQPLDPDGRVKMWVYGVSGGSFLIMIFLVFTSYLVCKKPKPHQSTPRHQKPLT

ref: LAYDGDLDM*
     ||||||||||
que: LAYDGDLDM*

HTML-formatted protein alignment
svg_line none SP ENST00000272643.THSD7B.118 ta tt SVG inactivating mutations visualization
ref_linkENST00000272643Reference transcript link
inact_mut_html_table
141SSM('gt', 'gc')->taNOSSM_1
150SSM('ag',)->ttNOSSM_2
HTML-formatted inactivating mutations table
exon_ali_html
Exon number: 1

Exon region: chr1:129358567-129358706
Nucleotide percent identity: 83.45 | BLOSUM: 70.92
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129358551-129358747): YES

Sequence alignment between reference and query exon:
ref: ATGTTTCCAAAGAGCAACCTAACAGTCACTTGCTGGGTATGGAGGAGCATGAGGAAGCTCTTTCTATTGCTTTCTCTCTT
     |||||||  | |||  | ||  | ||||||  |||||| |  |||||||||||||||||||||||| ||||||||||| |
que: ATGTTTCTGAGGAGTGATCTGGCTGTCACTCACTGGGTTTCCAGGAGCATGAGGAAGCTCTTTCTAGTGCTTTCTCTCCT

ref: GCTGTCCCATGCAGCTCATTTGGAAGGCAAAAAGGATAATCAGTTCATCTGGAAACCAG
     ||||||||| |||||||||||||||||||  ||||| ||||||||| |||||||| | |
que: GCTGTCCCAAGCAGCTCATTTGGAAGGCAGGAAGGACAATCAGTTCCTCTGGAAAACCG


Exon number: 2

Exon region: chr1:129523106-129523917
Nucleotide percent identity: 80.02 | BLOSUM: 83.43
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129523103-129523992): YES

Sequence alignment between reference and query exon:
ref: GTCCGTGGGGAAGGTGTACAGGAGACTGTGGTCCCGGAGGAGTCCAGAGTCGGGCAGTGTGGTGTTTTCATGTTGACGGG
     |||| |||||||||||| |||| ||||| || || || |||| ||| ||||| || || ||||| |||||  | || |||
que: GTCCCTGGGGAAGGTGTGCAGGTGACTGCGGACCAGGCGGAGCCCAAAGTCGTGCTGTATGGTGCTTTCACATAGAAGGG

ref: TGGACAAGTCACCTGTCTAACTGTGGTGAGAGCAACAGGCCTCCAAAGGAAAGAAGTTGTTTCCGAGTTTGTGACTGGCA
     ||||| |||| | |||| ||||||| |||||||| |   |||||||||||||| || |||||||| || |||||||||||
que: TGGACGAGTCCCATGTCGAACTGTGATGAGAGCAGCCAACCTCCAAAGGAAAGGAGCTGTTTCCGCGTGTGTGACTGGCA

ref: CAGTGACCTCTTTCAGTGGGAGGTTTCTGACTGGCACCACTGTGTGCTTGTTCCTTACGCTCGCGGTGAAGTCAAGCCTC
     ||||||||| || |||||||||||||| |||||||| | |||  | || ||||||   || |  |||||   || |||||
que: CAGTGACCTGTTCCAGTGGGAGGTTTCCGACTGGCATCGCTGCCTTCTGGTTCCTGGGGCCCAAGGTGAGCCCAGGCCTC

ref: GGACTGCAGAGTGTGTGACGGCTCAGCATGGACTGCAGCACCGGATGGTGCGCTGCATTCAGAAGCTGAACCGAACTGTG
     || |||  || |||||||| || ||||| || || ||||||||||  ||||||||  |||||||||| ||  ||||  ||
que: GGGCTGTGGAATGTGTGACTGCACAGCACGGTCTACAGCACCGGACAGTGCGCTGTCTTCAGAAGCTCAATAGAACCATG

ref: GTTGCAAATGAAATATGCGAACACTTTGCCCTTCAGCCTCCTACAGAACAGGCTTGCCTCATTCCTTGTCCCCGGGATTG
     ||  | ||||| || || ||||||||||| | |||||| || ||||| || || |||||||||||||| ||| |||| ||
que: GTGTCCAATGAGATCTGTGAACACTTTGCTCCTCAGCCCCCCACAGAGCAAGCCTGCCTCATTCCTTGCCCCAGGGACTG

ref: TGTAGTATCTGAGTTCTTACCATGGTCCAACTGTAGCAAGGGATGTGGGAAGAAATTGCAGCATAGAACTCGCGCGGTCA
      || |||||||||||||  |||||||||| |||   | | ||||||||||||||| |||||||||||||||| | || ||
que: CGTGGTATCTGAGTTCTCCCCATGGTCCACCTGCCCCGAAGGATGTGGGAAGAAACTGCAGCATAGAACTCGTGTGGCCA

ref: TAGCTCCCCCTCTCTTTGGTGGTTTGCAATGTCCAAATCTGACTGAGTCAAGAGCCTGTGATGCTCCCATTTCCTGTCCT
     | || |||||||| | ||| ||| |||| ||||||||||| || ||||| |||||||| || |||||  |||||||||||
que: TCGCGCCCCCTCTGTATGGAGGTCTGCAGTGTCCAAATCTCACGGAGTCCAGAGCCTGCGAGGCTCCAGTTTCCTGTCCT

ref: CTTGGGGAAGAGGAATATACATTTAGCCTTAAGGTTGGACCATGGAGTAAATGCAGACTGCCTCATCTTAAAGAAATTAA
     |||||| |||| |||||| | || ||||| ||||| ||||||||||| ||||| ||||| ||||| ||||| ||| |  |
que: CTTGGGAAAGAAGAATATTCCTTCAGCCTAAAGGTGGGACCATGGAGCAAATGTAGACTCCCTCACCTTAAGGAAGTCGA

ref: TCCAAGCGGAAGAACTGTTCTGGATTTTAACTCTGATTCAAATGAGCGAGTCACCTTTAAACATCAAAGTTACAAAGCAC
      |  |||||||||| | | | |||||||| |||||||||||| |||| ||||||| | | |||||| |||||||||||||
que: CCTCAGCGGAAGAAATATCCAGGATTTTAGCTCTGATTCAAACGAGCAAGTCACCCTAACACATCAGAGTTACAAAGCAC

ref: ATCATCATTCGAAGTCTTGGGCAATAGAGATAGGTTATCAAACCCGGCAGGTTTCGTGTACAAGAAGTGATGGACAAAAT
     | || || ||  || || |||   ||| |||||| | ||||||| ||||||| | |||||| ||||||||||||  ||| 
que: ACCACCACTCCCAGCCTGGGGATGTAGTGATAGGGTTTCAAACCAGGCAGGTGTGGTGTACCAGAAGTGATGGAAGAAAC

ref: GCTATGTTAAG
     ||  |||||||
que: GCCCTGTTAAG


Exon number: 3

Exon region: chr1:129540846-129541095
Nucleotide percent identity: 81.93 | BLOSUM: 86.06
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129540838-129541117): YES

Sequence alignment between reference and query exon:
ref: CCTTTGCCTTCAAGATTCCTTCCCATTGACTGTTCAGTCCTGCATCATGCCCAAAGACTGTGAAACCTCCCAGTGGTCCT
     ||||||  |||  |||||||||||  ||||||| ||| | ||  | ||||| ||||||||||| || ||  | |||||  
que: CCTTTGTGTTCGTGATTCCTTCCCTCTGACTGTCCAGCCTTGTGTGATGCCAAAAGACTGTGAGACTTCTGAATGGTCTC

ref: CCTGGAGCCCCTGCTCCAAGACATGCCGTTCAGGGAGTCTCTTGCCAGGATTTAGGAGCAGGAGCCGGAACGTGAAGCAC
     | ||||||||||| |||||||| |||||||| |||| | | |  || ||| |||| ||||||||||||||||||||||| 
que: CATGGAGCCCCTGTTCCAAGACCTGCCGTTCTGGGACTTTATCACCTGGAGTTAGAAGCAGGAGCCGGAACGTGAAGCAT

ref: ATGGCTATTGGAGGTGGAAAGGAGTGTCCTGAACTTCTTGAGAAAGAGGCCTGCATTGTTGAAGGAGAACTTCTGCAGCA
     || ||||||||||||||  |||| || || |||||||||||||||||| ||||||||| |||||| ||| ||||||| | 
que: ATTGCTATTGGAGGTGGCCAGGAATGCCCAGAACTTCTTGAGAAAGAGACCTGCATTGCTGAAGGGGAATTTCTGCAACC

ref: ATGTCCCAG
     |||||||||
que: ATGTCCCAG


Exon number: 4

Exon region: chr1:129556613-129556783
Nucleotide percent identity: 84.71 | BLOSUM: 85.53
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129556547-129556802): YES

Sequence alignment between reference and query exon:
ref: GTATTCCTGGAGAACTTCTGAATGGAAAGAATGCCAAGTCTCTCTCCTCCTCGAGCAGCAGGATCCCCACTGGCATGTGA
     ||||||||||||||| ||||||||||| ||||||||||||||||| || || ||||| || ||||| |  ||||||| ||
que: GTATTCCTGGAGAACCTCTGAATGGAAGGAATGCCAAGTCTCTCTTCTTCTGGAGCAACACGATCCACTTTGGCATGAGA

ref: CGGGACCCGTGTGTGGCGGTGGGATCCAGACCCGGGAGGTGTACTGTGCCCAGAGCGTACCAGCAGCTGCCGCACTGAGG
     | |||||  | ||||| ||||||||||||||||||||||||||||||||||||||| |||||||| |    |||   |||
que: CAGGACCAATCTGTGGTGGTGGGATCCAGACCCGGGAGGTGTACTGTGCCCAGAGCCTACCAGCAACCATTGCATCAAGG

ref: GCCAAGGAAG
      |||||||||
que: ACCAAGGAAG


Exon number: 5

Exon region: chr1:129595550-129595706
Nucleotide percent identity: 82.05 | BLOSUM: 82.49
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129595482-129595716): YES

Sequence alignment between reference and query exon:
ref: TCTCTAGACCTGTGGAAAAGGCATTATGTGTGGGACCCGCCCCGTTGCCCTCTCAGCTCTGCAATATCCCTTGCTCTACG
     |||| || || ||||||| | || ||||  ||||||| ||||| |   |||||||||| |||||| |||||||||| | |
que: TCTCCAGGCCCGTGGAAAGGACACTATGCTTGGGACCTGCCCCCTCAGCCTCTCAGCTTTGCAATGTCCCTTGCTCGATG

ref: GACTGCATAGTATCTTCCTGGTCAGCCTGGGGCCTGTGCATCCATGAAAACTGTCATGATCCTCAGGGGAAAAAAG
     |||||||||||||||||||||||| |||||||||  ||  |   ||| ||||| ||||||||||||||||| ||||
que: GACTGCATAGTATCTTCCTGGTCAACCTGGGGCCCATGTGTTTTTGAGAACTGCCATGATCCTCAGGGGAAGAAAG


Exon number: 6

Exon region: chr1:129605785-129605983
Nucleotide percent identity: 83.84 | BLOSUM: 87.80
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129605732-129605998): YES

Sequence alignment between reference and query exon:
ref: GATTTAGAACGAGGCAGCGCCATGTCCTCATGGAATCTACAGGGCCTGCAGGGCATTGCCCTCATTTGGTGGAGTCTGTT
     | ||||||| ||| ||||||||||| |||||||| |||||||||||    ||||  ||||||||| |||  || ||||| 
que: GCTTTAGAATGAGACAGCGCCATGTACTCATGGAGTCTACAGGGCCCATGGGGCGCTGCCCTCATCTGGCAGAATCTGTA

ref: CCTTGTGAGGATCCAATGTGCTACCGATGGCTGGCATCAGAAGGGATCTGTTTCCCTGATCATGGAAAATGTGGCCTGGG
     ||||||||||||||||||||  | || ||||| || || |||||||||||| |  |||||||||| ||||||||||||||
que: CCTTGTGAGGATCCAATGTGTCATCGCTGGCTTGCCTCGGAAGGGATCTGTATTGCTGATCATGGGAAATGTGGCCTGGG

ref: ACATCGTATTCTGAAGGCCGTCTGCCAGAATGACCGCG
     |||||| ||||||||||| ||||| |||||||| || |
que: ACATCGCATTCTGAAGGCTGTCTGTCAGAATGAGCGAG


Exon number: 7

Exon region: chr1:129686182-129686374
Nucleotide percent identity: 85.94 | BLOSUM: 91.12
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129686132-129686386): YES

Sequence alignment between reference and query exon:
ref: GAGAAGATGTATCAGGGAGTCTTTGCCCAGTTCCCCCTCCTCCTGAGAGGAAGTCTTGTGAAATTCCCTGCCGAATGGAC
     ||||||| ||||||||| |||| || ||||| || |||||||||||  | | | ||||||||||||| ||||||||||||
que: GAGAAGAAGTATCAGGGGGTCTCTGTCCAGTGCCTCCTCCTCCTGAACGAATGGCTTGTGAAATTCCTTGCCGAATGGAC

ref: TGTGTGCTGAGCGAGTGGACGGAGTGGTCATCCTGTTCCCAGTCCTGTTCAAATAAAAACTCAGATGGGAAACAGACCAG
     |||||  |||| |||||||| | |||||||||||| || ||||||||||||||||||||||||||||||||||| |||||
que: TGTGTAGTGAGTGAGTGGACAGTGTGGTCATCCTGCTCTCAGTCCTGTTCAAATAAAAACTCAGATGGGAAACAAACCAG

ref: GTCAAGAACTATCCTGGCACTGGCTGGGGAAG
     |||| |  ||||||| ||  ||||||| ||||
que: GTCACGTTCTATCCTCGCTTTGGCTGGAGAAG


Exon number: 8

Exon region: chr1:129688005-129688240
Nucleotide percent identity: 80.43 | BLOSUM: 84.55
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129687994-129688243): YES

Sequence alignment between reference and query exon:
ref: GTGGAAAGCCATGTCCCCCTAGTCAGGCTCTCCAAGAGCATCGTTTGTGTAATGACCATTCCTGTATGCAGCTTCACTGG
     |||||||| | || ||   ||||||||  ||||||||| | ||  | || ||||| ||||||||||  |||||  |||||
que: GTGGAAAGACCTGCCCTAGTAGTCAGGAACTCCAAGAGTACCGCCTATGCAATGATCATTCCTGTACACAGCTCTACTGG

ref: GAGACATCGCCTTGGGGCCCTTGTTCTGAGGACACATTGGTAACTGCCCTTAATGCAACCATTGGCTGGAATGGAGAAGC
     ||||||||  |||||||  | || |||||  | ||  | || ||||| || ||||  |||||||||||||||||||||||
que: GAGACATCTGCTTGGGGTTCCTGCTCTGAAAATACTCTTGTGACTGCTCTCAATGTGACCATTGGCTGGAATGGAGAAGC

ref: CACGTGTGGTGTAGGCATTCAGACTCGGAGAGTCTTCTGTGTCAAGAGTCACGTGGGACAAGTAATGACCAAAAG
      || ||||| || ||||||||||| || |  ||||||||| |||||||||| |||||||||||||||||||||||
que: AACATGTGGGGTGGGCATTCAGACACGAAAGGTCTTCTGTATCAAGAGTCATGTGGGACAAGTAATGACCAAAAG


Exon number: 9

Exon region: chr1:129704029-129704145
Nucleotide percent identity: 83.62 | BLOSUM: 92.11
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129704003-129704185): YES

Sequence alignment between reference and query exon:
ref: ATGTCCAGATTCTACTCGACCTGAAACTGTGCGCCCCTGTTTTCTCCCATGCAAAAAAGACTGTATTGTGACTGCTTTCA
     ||||||||| ||||| || || ||||||||  | || ||||| ||||||||||| ||||||||  |||||||||||||||
que: ATGTCCAGAGTCTACACGGCCAGAAACTGTAAGACCTTGTTTCCTCCCATGCAAGAAAGACTGCCTTGTGACTGCTTTCA

ref: GTGAGTGGACACCCTGCCCAAGGATGTGCCAAGCAG
     ||||||||||||| |||||| ||   |||||  |||
que: GTGAGTGGACACCATGCCCACGGCCCTGCCAGCCAG


Exon number: 10

Exon region: chr1:129744379-129744509
Nucleotide percent identity: 82.31 | BLOSUM: 92.89
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129744350-129744525): YES

Sequence alignment between reference and query exon:
ref: GAAATGCCACAGTAAAACAGTCTCGATACAGAATCATCATCCAAGAAGCAGCCAATGGAGGCCAGGAATGCCCAGATACC
     ||||| | ||| ||||||| ||||||||||| || |||||||| |||||||||||||| || || || |||||||| |||
que: GAAATACTACAATAAAACAATCTCGATACAGGATTATCATCCAGGAAGCAGCCAATGGGGGTCAAGAGTGCCCAGACACC

ref: TTATATGAGGAGAGAGAGTGTGAAGATGTTTCCTTGTGTCCTGTATATCG
     || | ||| || ||||||||||||||| | ||  ||||||||  ||| ||
que: TTGTTTGAAGAAAGAGAGTGTGAAGATATCTCACTGTGTCCTTCATACCG


Exon number: 11

Exon region: chr1:129750328-129750432
Nucleotide percent identity: 82.69 | BLOSUM: 83.08
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129750262-129750437): YES

Sequence alignment between reference and query exon:
ref: GTGGAAGCCACAGAAATGGAGCCCTTGCATCTTAGTGCCAGAGTCTGTCTGGCAGGGAATAACGGGCAGCAGTGAAGCCT
     ||||||||| |||||||||||| |||| ||| | || ||||||||| || ||||||| | ||| |||| |||||| || |
que: GTGGAAGCCGCAGAAATGGAGCTCTTGTATCCTGGTTCCAGAGTCTATCAGGCAGGGGAGAACAGGCACCAGTGAGGCAT

ref: GTGGAAAGGGGTTACAAACAAGAG
     |||| |||||| | || |||||||
que: GTGGGAAGGGGCTGCAGACAAGAG


Exon number: 12

Exon region: chr1:129843289-129843484
Nucleotide percent identity: 83.59 | BLOSUM: 86.36
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:129843185-129843501): YES

Sequence alignment between reference and query exon:
ref: CTGTCTCATGCATCTCTGATGACAACCGGTCAGCAGAAATGATGGAATGCCTCAAGCAGACAAACGGCATGCCTCTCCTT
     |||||||||||||||||||||| |||| ||| ||||||||||  || |||||||||||||  || |||||||||| ||||
que: CTGTCTCATGCATCTCTGATGATAACCAGTCTGCAGAAATGACAGAGTGCCTCAAGCAGATGAATGGCATGCCTCCCCTT

ref: GTGCAAGAATGCACAGTCCCATGTCGAGAAGACTGCACCTTCACTGCTTGGTCCAAGTTTACGCCCTGCTCCACGAACTG
     ||||| ||||||||  | || ||||| || ||||||||||||||  ||||||| ||||| || |||||||||| ||||||
que: GTGCAGGAATGCACCATTCCCTGTCGGGACGACTGCACCTTCACCCCTTGGTCTAAGTTCACTCCCTGCTCCAAGAACTG

ref: TGAAGCCACAAAAAGTAGGCGGCGACAGCTCACAG
     |||||| ||  | |  ||| |||| ||||| ||||
que: TGAAGCAACTCAGATCAGGAGGCGGCAGCTAACAG


Exon number: 13

Exon region: chr1:129848984-129849251
Nucleotide percent identity: 82.40 | BLOSUM: 77.85
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129848898-129849283): YES

Sequence alignment between reference and query exon:
ref: GGAAAAGCAGAAAGAAGGAGAAATGCCAGGATTCTGACCTTTACCCTCTAGTGGAGACAGAACTATGTCCTTGTGATGAA
     |||||||||| ||||| ||||| ||||||||| |   ||| |||||||| ||||| |  |||| |||||| ||||||   
que: GGAAAAGCAGGAAGAAAGAGAAGTGCCAGGATGCGTCCCTGTACCCTCTGGTGGAAATGGAACCATGTCCCTGTGATACG

ref: TTTATATCCCAACCTTATGGAAACTGGTCAGATTGCATTCTTCCAGAAGGCAGAAGGGAGCCTCACCGAGGA---CTGCG
     ||||| || || ||||||||||||||||||| ||||||||| |||||||||| ||||||  |||| | ||||    || |
que: TTTATGTCTCATCCTTATGGAAACTGGTCAGCTTGCATTCTACCAGAAGGCAAAAGGGATGCTCAGCAAGGAGGATTGTG

ref: GGTACAAGCAGACAGCAAAGAATGTGGAGAAGGCCTGCGCTTTCGAGCAGTAGCCTGTTCTGATAAAAATGGAAGACCTG
     ||| |||| |||   ||||||||||||||||||| |||||||||||||| |||| || ||  ||| |||||||||||| |
que: GGTGCAAGGAGATGACAAAGAATGTGGAGAAGGCGTGCGCTTTCGAGCAATAGCATGCTCCAATATAAATGGAAGACCGG

ref: TTGACCCCTCCTTCTGCAGCAGCTCTG
     |||||||||| ||||||| ||||||||
que: TTGACCCCTCATTCTGCAACAGCTCTG


Exon number: 14

Exon region: chr1:129879126-129879306
Nucleotide percent identity: 90.00 | BLOSUM: 96.80
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:129879112-129879340): YES

Sequence alignment between reference and query exon:
ref: GTTACATTCAAGAAAAATGTGTCATTCCCTGCCCATTTGATTGCAAGTTAAGCGATTGGTCTAGTTGGGGGTCTTGCAGT
     |||||||||| |||  ||||||||| ||||| || |||||||||||| |||| || ||||| || ||||| |||||||| 
que: GTTACATTCAGGAAGCATGTGTCATCCCCTGTCCGTTTGATTGCAAGCTAAGTGACTGGTCCAGCTGGGGTTCTTGCAGC

ref: TCATCTTGTGGAATTGGAGTGAGAATTCGATCCAAATGGCTAAAAGAAAAACCTTACAATGGAGGACGACCATGTCCCAA
     ||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||| |||||| || |||||||||||
que: TCATCTTGTGGGATTGGAGTGAGAATTCGATCAAAATGGCTAAAAGAAAAACCTTACAGTGGAGGTCGGCCATGTCCCAA

ref: ACTGGATCTCAAGAATCAGG
     ||||||||||||||||||||
que: ACTGGATCTCAAGAATCAGG


Exon number: 15

Exon region: chr1:130030802-130030941
Nucleotide percent identity: 88.49 | BLOSUM: 89.06
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130030781-130030959): YES

Sequence alignment between reference and query exon:
ref: GACAGGTACATGAGGCAGTCCCATGTTACAGTGAGTGCAATCAGTATTCCTGGGTTGTAGAACACTGGTCTTCATGCAAA
      |||||| |||||||||||||||||||||||||||||  |||| ||||||||||| ||||||||||||||| ||||||| 
que: TACAGGTTCATGAGGCAGTCCCATGTTACAGTGAGTGTGATCAATATTCCTGGGTCGTAGAACACTGGTCTCCATGCAAG

ref: ATCAACAATGAGCTGAGGTCCCTGCGCTGTGGAGGAGGAACACAATCTAGGAAAATCAG
     ||||| ||||||||||| ||||  ||||||||| |||||||||| ||||| | ||||||
que: ATCAATAATGAGCTGAGATCCCCACGCTGTGGAAGAGGAACACAGTCTAGAAGAATCAG


Exon number: 16

Exon region: chr1:130044296-130044447
Nucleotide percent identity: 84.11 | BLOSUM: 78.35
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130044285-130044456): YES

Sequence alignment between reference and query exon:
ref: ATGTGTGAATACTGCGGATGGTGAAGGTGGAGCAGTGGATAGCAACCTGTGCAACCAGGATGAAATTCCCCCAGAAACCC
      ||||||| |||||| ||  | ||||| || |||||| | || | ||||||||||||||||||   ||||| ||||||||
que: GTGTGTGAGTACTGCTGACAGAGAAGGAGGGGCAGTGAACAGGAGCCTGTGCAACCAGGATGATGCTCCCCAAGAAACCC

ref: AGTCCTGTTCTCTTATGTGTCCCAATGAGTGTGTCATGTCTGAGTGGGGACTTTGGAGCAAATGCCCACAG
     || ||||||||||| ||||||||| ||||||||||||||| |||||||||   ||||||| ||||||||||
que: AGGCCTGTTCTCTTCTGTGTCCCAGTGAGTGTGTCATGTCCGAGTGGGGAACATGGAGCAGATGCCCACAG


Exon number: 17

Exon region: chr1:130087310-130087452
Nucleotide percent identity: 86.62 | BLOSUM: 95.02
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130087302-130087465): YES

Sequence alignment between reference and query exon:
ref: TCATGCGATCCCCACACAATGCAGAGAAGAACTCGCCACCTGCTAAGACCATCACTGAACTCAAGGACTTGTGCTGAAGA
     ||||| || |||||  ||||||||||||||||||| || ||||| || || |||||||||||||| |||||||  |||||
que: TCATGTGACCCCCATGCAATGCAGAGAAGAACTCGGCATCTGCTGAGGCCCTCACTGAACTCAAGAACTTGTGGGGAAGA

ref: CTCACAGGTGCAGCCTTGCCTCCTGAATGAAAATTGCTTCCAGTTCCAGTACAATCTAACAG
     ||| ||||||| ||| |||||||| |||||||| || |||||||||||||||||||| ||||
que: CTCGCAGGTGCGGCCCTGCCTCCTCAATGAAAACTGTTTCCAGTTCCAGTACAATCTGACAG


Exon number: 18

Exon region: chr1:130090556-130090672
Nucleotide percent identity: 87.93 | BLOSUM: 82.71
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130090541-130090675): YES

Sequence alignment between reference and query exon:
ref: AGTGGAGCACATGCCAGCTGAGTGAAAACGCACCCTGTGGTCAAGGCGTCAGGACCCGCCTGCTAAGCTGTGTGTGCAGT
     |||||||||||||||||||||||||||| |   ||||||| || || || |||||||||||||| ||||||||| |||||
que: AGTGGAGCACATGCCAGCTGAGTGAAAATGTTTCCTGTGGCCAGGGTGTGAGGACCCGCCTGCTGAGCTGTGTGCGCAGT

ref: GATGGCAAGCCAGTCAGCATGGACCAATGTGAGCAG
     ||||||||| | |||||||||||||| || ||||||
que: GATGGCAAGTCTGTCAGCATGGACCACTGCGAGCAG


Exon number: 19

Exon region: chr1:130092785-130092903
Nucleotide percent identity: 87.29 | BLOSUM: 91.34
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130092777-130092908): YES

Sequence alignment between reference and query exon:
ref: CATAATTTGGAGAAGCCCCAGAGAATGAGCATTCCCTGCTTGGTGGAATGCGTGGTCAACTGTCAGCTCTCAGGGTGGAC
     | |||| |||| || |||||||| ||||| ||||||||  |||||||||| ||||||||||||||||||||||| |||||
que: CGTAATCTGGAAAAACCCCAGAGGATGAGTATTCCCTGTCTGGTGGAATGTGTGGTCAACTGTCAGCTCTCAGGATGGAC

ref: GGCTTGGACAGAGTGTTCACAGACCTGTGGCCATGGAG
       | ||||||||||||||||| ||||||||||| ||||
que: AACATGGACAGAGTGTTCACAAACCTGTGGCCAAGGAG


Exon number: 20

Exon region: chr1:130108088-130108234
Nucleotide percent identity: 92.47 | BLOSUM: 93.80
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130108064-130108259): YES

Sequence alignment between reference and query exon:
ref: GTCGAATGAGCCGGACTCGATTTATCATTATGCCAACCCAAGGAGAAGGACGGCCATGCCCCACAGAGCTTACCCAGGAG
     |||| |||||||||||||||||||||||||||||||||||||||||||| || | |||||||||||| || |||||| ||
que: GTCGCATGAGCCGGACTCGATTTATCATTATGCCAACCCAAGGAGAAGGTCGACAATGCCCCACAGAACTCACCCAGCAG

ref: AAAACCTGCCCAGTGACCCCCTGCTACAGCTGGGTCCTTGGCAACTGGTCTGCATGTAAATTGGAG
     ||| ||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||||
que: AAACCCTGCCCAGTGACACCCTGCTATAGTTGGGTCCTTGGCAACTGGTCTGCATGTAAATTGGAG


Exon number: 21

Exon region: chr1:130116196-130116356
Nucleotide percent identity: 80.62 | BLOSUM: 83.28
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130116148-130116366): YES

Sequence alignment between reference and query exon:
ref: GGTGGAGACTGTGGGGAAGGAGTTCAGATCCGCAGCCTTTCCTGCATGGTCCACAGTGGTTCAATATCTCATGCAGCTGG
     || ||||| ||||| |||||||| ||| | |||||| | |||||  | ||||||| ||| |||||||| ||  | |||| 
que: GGCGGAGATTGTGGAGAAGGAGTCCAGGTGCGCAGCTTCTCCTGTGTAGTCCACAATGGCTCAATATCCCACACGGCTGT

ref: ACGTGTCGAGGATGCACTGTGTGGAGAAATGCCCTTTCAGGACAGCATCCTGAAGCAGCTGTGTTCTGTGCCTTGCCCAG
      | ||| ||||| || |||||||||||| | ||||| || ||  | ||||||||||||||||| ||||||||||||||||
que: CCCTGTGGAGGAGGCCCTGTGTGGAGAAGTACCCTTCCAAGAAGGAATCCTGAAGCAGCTGTGCTCTGTGCCTTGCCCAG


Exon number: 22

Exon region: chr1:130117592-130117766
Nucleotide percent identity: 85.06 | BLOSUM: 94.34
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130117462-130117817): YES

Sequence alignment between reference and query exon:
ref: GAGACTGCCATTTAACAGAATGGTCAGAGTGGAGCACATGTGAATTAACCTGCATTGATGGAAGAAGCTTTGAGACTGTG
     ||||||||||  | ||   |||||| ||||||||||  |||||  ||||||||||||| ||||||||||| |||||    
que: GAGACTGCCACATTACCCCATGGTCTGAGTGGAGCAAGTGTGAGCTAACCTGCATTGACGGAAGAAGCTTCGAGACCACA

ref: GGCCGCCAGTCTAGATCAAGGACTTTTATAATTCAGTCTTTTGAGAACCAAGACAGCTGCCCCCAACAGGTTCTAGAAAC
     |||||||| ||||| |||||||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||
que: GGCCGCCAATCTAGGTCAAGGACATTCATAATCCAGTCTTTTGAGAATCAAGATAGCTGCCCCCAACAGGTTCTAGAAAC

ref: ACGCCCTTGTACAG
     ||| || |||||||
que: ACGACCATGTACAG


Exon number: 23

Exon region: chr1:130117867-130117963
Nucleotide percent identity: 91.67 | BLOSUM: 95.21
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130117823-130118022): YES

Sequence alignment between reference and query exon:
ref: GAGGCAAATGTTATCACTACACATGGAAAGCAAGTCTTTGGAACAATAACGAACGAACTGTATGGTGCCAGCGTTCAGAT
     | ||||||||||||||||||| ||||||||||||||||||||||||||| || || ||||| ||||||||||| ||||||
que: GTGGCAAATGTTATCACTACATATGGAAAGCAAGTCTTTGGAACAATAATGAGCGGACTGTGTGGTGCCAGCGCTCAGAT

ref: GGCGTTAATGTCACAG
     ||| ||||||||||||
que: GGCCTTAATGTCACAG


Exon number: 24

Exon region: chr1:130120290-130120373
Nucleotide percent identity: 90.36 | BLOSUM: 98.06
Intersects assembly gaps: NO
Exon alignment class: A
Detected within expected region (exp:130120247-130120422): YES

Sequence alignment between reference and query exon:
ref: GAGGCTGCTCCCCTCAGGCCCGTCCTGCTGCCATTCGGCAGTGCATTCCAGCCTGCAGAAAACCTTTCTCCTACTGTACA
     | ||||||||||||||||| || |||||||| |||||||| ||||||||||| |||| |||||||||||||||||| |||
que: GTGGCTGCTCCCCTCAGGCACGCCCTGCTGCTATTCGGCAATGCATTCCAGCATGCAAAAAACCTTTCTCCTACTGCACA

ref: CAG
     |||
que: CAG


Exon number: 25

Exon region: chr1:130122843-130123036
Nucleotide percent identity: 90.16 | BLOSUM: 97.75
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130122809-130123147): YES

Sequence alignment between reference and query exon:
ref: GGTGGAGTCTGTGGTTGTGAGAAGGGCTATACAGAGATAATGAAATCAAATGGTTTCCTGGATTACTGCATGAAAGTACC
     || ||||||||||| ||||||||||| || ||||||||||||| ||||| ||| |||||||||||||||||||| || ||
que: GGAGGAGTCTGTGGCTGTGAGAAGGGATACACAGAGATAATGAGATCAAGTGGCTTCCTGGATTACTGCATGAAGGTGCC

ref: AGGCTCAGAGGATAAAAAAGCTGATGTGAAAAACCTTTCTGGGAAAAACAGACCTGTGAATTCAAAAATACATGATATTT
      ||||| ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||
que: TGGCTCGGAGGATAAAAAAGCTGACGTGAAAAACCTCTCTGGGAAAAATAGACCTGTGAATTCCAAAATACATGATATTT

ref: TTAAAGGATGGTCTCTTCAACCACTTGATCCAG
     |||||||||||||||| ||||| || || ||||
que: TTAAAGGATGGTCTCTCCAACCTCTGGACCCAG


Exon number: 26

Exon region: chr1:130137977-130138065
Nucleotide percent identity: 90.91 | BLOSUM: 95.10
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130137951-130138085): YES

Sequence alignment between reference and query exon:
ref: ATGGCCGAGTAAAAATTTGGGTTTATGGCGTTTCAGGTGGCGCTTTTCTCATCATGATTTTCCTAATATTTACTTCCTAC
     |||||||||||||||| ||||||||||||||||| ||||||  |||||| |||||||| |||||| ||||||||||||| 
que: ATGGCCGAGTAAAAATGTGGGTTTATGGCGTTTCCGGTGGCAGTTTTCTTATCATGATCTTCCTAGTATTTACTTCCTAT

ref: CTTGTTTG
     ||||||||
que: CTTGTTTG


Exon number: 27

Exon region: chr1:130145835-130145917
Nucleotide percent identity: 93.90 | BLOSUM: 90.34
Intersects assembly gaps: NO
Exon alignment class: A+
Detected within expected region (exp:130145820-130145952): YES

Sequence alignment between reference and query exon:
ref: CAAGAAGCCAAAACCACATCAAAGCACACCTCCCCAACAGAAGCCTCTGACCTTAGCCTACGATGGAGACTTAGACATGT
     |||||||||||||||||||||||||||||||| ||| |||||||| |||||||| ||||||||||||||||| |||||||
que: CAAGAAGCCAAAACCACATCAAAGCACACCTCGCCATCAGAAGCCACTGACCTTGGCCTACGATGGAGACTTGGACATGT

ref: AA
     ||
que: AA


HTML-formatted exon alignment

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizeschromStartsref_trans_idref_regionquery_regionchain_scorechain_syntenychain_flankchain_gl_cds_fractchain_loc_cds_fractchain_exon_covchain_intron_covstatusperc_intact_ign_Mperc_intact_int_Mintact_codon_propouf_propmid_intactmid_presprot_alignmentsvg_lineref_linkinact_mut_html_tableexon_ali_html
chr1129358567130145917ENST00000272643.THSD7B.1181000+1293585671301459170,0,20027139,811,249,170,156,198,192,235,116,130,104,195,267,180,139,151,142,116,118,146,160,174,96,83,193,88,82,0,164539,182279,198046,236983,247218,327615,329438,345462,385812,391761,484722,490417,520559,672235,685729,728743,731989,734218, ...ENST00000272643.THSD7Bchr2:136882178-137677717chr1:129358567-1301459170.9963686466217041880.43590.0192131090514080920.0124529499327948321.00.4847922998986829Intact1.01.01.00.011ref: MFPKSNLTVTCWVWRSMRKLFLLLSLLLSHAAHLEGKKDNQFIWKPGPWGRCTGDCGPGGVQSRAVWCFHVDGWTSHLSN      ... ...ENST00000272643141SSM('gt', 'gc')->taNOSSM_1150SSM ...Exon number: 1Exon region: chr1:129358567-129358706Nucleotide percent identity: 83.45 | BL ...
chr1129358567130145917ENST00000409968.THSD7B.1181000+1293585671301459170,0,20027139,811,249,170,156,198,192,235,116,130,104,195,267,179,134,151,142,116,118,146,160,174,96,83,193,88,82,0,164539,182279,198046,236983,247218,327615,329438,345462,385812,391761,484722,490417,520559,672240,685729,728743,731989,734218, ...ENST00000409968.THSD7Bchr2:136765544-137677718chr1:129358567-1301459170.9963686466217041880.539050.0192131090514080920.010375037929899091.00.507528182398114Intact1.01.01.00.011ref: MFPKSNLTVTCWVWRSMRKLFLLLSLLLSHAAHLEGKKDNQFIWKPGPWGRCTGDCGPGGVQSRAVWCFHVDGWTSHLSN      ... ...ENST00000409968Exon number: 1Exon region: chr1:129358567-129358706Nucleotide percent identity: 83.45 | BL ...
chr1129523106130145917ENST00000413152.THSD7B.1181000+129523106130145917255,160,12026811,249,170,156,198,192,235,116,130,104,195,267,180,137,151,142,116,118,146,160,174,96,83,193,88,82,0,17740,33507,72444,82679,163076,164899,180923,221273,227222,320183,325878,356020,507698,521190,564204,567450,569679,584982,5930 ...ENST00000413152.THSD7Bchr2:136990891-137677717chr1:129523106-1301459170.9963686466217041880.357050.0192131090514080920.0137587592100785090.99915504858470640.4978868689241975Uncertain Loss0.63371356147021550.63371356147021550.98986058301647650.001ref: MHNTADEVVLYHKLAGPWGRCTGDCGPGGVQSRAVWCFHVDGWTSHLSNCGESNRPPKERSCFRVCDWHSDLFQWEVSDW      ... ...ENST0000041315210Deleted exon-YESDEL_1141SSM( ...Exon number: 1Exon region: chr1:129477246-129477262Nucleotide percent identity: 23.91 | BL ...
chr1130319230130390406ENST00000367064.CD55.81000-130319230130390406255,160,120968,81,171,192,86,100,192,186,100,0,56834,57593,60890,65327,66593,68088,70328,71076,ENST00000367064.CD55chr1:207321677-207360966chr1:130319230-1303904060.99613451957702643790.16310.033829119985609410.10177031320926010.97818499127399650.2695986266655767Uncertain Loss0.83507853403141360.83507853403141360.96073298429319380.001ref: M-----TVARPSVPAALPLLGELPRLLLLVLLCL-PAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPG      ... ...ENST0000036706471SSM('gt', 'gc')->aaYESSSM_190Deleted ...Exon number: 1Exon region: chr1:130390406-130390306Nucleotide percent identity: 41.53 | BL ...
chr1130319230130390406ENST00000367067.CD55.81000-1303192301303904060,0,200968,475,278,192,86,100,192,186,100,0,56834,57645,60890,65327,66593,68088,70328,71076,ENST00000367067.CD55chr1:207321732-207359767chr1:130319230-1303904060.99636864662170413790.183750.033829119985609410.146164321379936460.97398669086509380.2598640583554377Intact0.96551724137931040.96551724137931040.96551724137931040.011ref: M-----TVARPSVPAALPLLGELPRLLLLVLLCL-PAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPG      ... ...ENST0000036706771SSM('gt', 'gc')->caNOSSM_180SSM ...Exon number: 1Exon region: chr1:130390406-130390306Nucleotide percent identity: 41.53 | BL ...
chr1130319230130390406ENST00000391921.CD55.81000-130319230130390406255,160,120868,81,171,192,86,100,186,100,0,56834,57593,60890,65327,66593,70328,71076,ENST00000391921.CD55chr1:207321642-207359713chr1:130319230-1303904060.99636864662170413790.18390.033829119985609410.08433953699500680.97379454926624740.27340001626412946Uncertain Loss0.80188679245283020.80188679245283020.95283018867924530.001ref: M-----TVARPSVPAALPLLGELPRLLLLVLLCL-PAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPG      ... ...ENST0000039192161SSM('gt', 'gc')->aaYESSSM_180Deleted ...Exon number: 1Exon region: chr1:130390406-130390306Nucleotide percent identity: 41.53 | BL ...
chr1130344575130345944ENST00000644836.CD55.2064931000-130344575130345944130,130,130286,100,0,1269,ENST00000644836.CD55chr1:207321747-207359876chr1:130344575-1303459440.689149081707000710.00.105084745762711860.105084745762711860.161038961038961040.043271594820521224Partial missing0.161038961038961041.01.00.838961038961038910ref: MTVAR-PSVPAALPLLGELPRLLLLVLLCLPAVWGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSV      ... ...ENST0000064483610Missing exon-YESMIS_120Missing exon ...Exon number: 1Exon region: chr1:130350695-130350601Nucleotide percent identity: 53.40 | BL ...
chr1130347337130347529ENST00000314754.CD55.2622331000-130347337130347529130,130,1301192,0,ENST00000314754.CD55chr1:207321700-207360501chr1:130347337-1303475290.63978749513626110.00.14534443603330810.14534443603330810.145124716553287990.030863016319947513Partial missing0.142857142857142850.7823129251700680.9843750.85487528344671200ref: MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWG--DCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDS      ... ...ENST0000031475410Missing exon-YESMIS_120Missing exon ...Exon number: 1Exon region: chr1:130349072-130349035Nucleotide percent identity: 18.00 | BL ...
chr1130347337130347529ENST00000367063.CD55.2622331000-130347337130347529130,130,1301192,0,ENST00000367063.CD55chr1:207321531-207340766chr1:130347337-1303475290.673902332782745410.00.14534443603330810.14534443603330810.143820224719101140.06435248518011856Partial missing0.141573033707865170.78426966292134840.9843750.856179775280898800ref: MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWG--DCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDS      ... ...ENST0000036706310Missing exon-YESMIS_120Missing exon ...Exon number: 1Exon region: chr1:130349072-130349035Nucleotide percent identity: 18.00 | BL ...
chr1130347337130347529ENST00000367064.CD55.2622331000-130347337130347529130,130,1301192,0,ENST00000367064.CD55chr1:207321677-207360966chr1:130347337-1303475290.63978749513626110.00.14534443603330810.14534443603330810.167539267015706820.030763781029455844Partial missing0.16492146596858640.74869109947643970.9843750.832460732984293200ref: MTVARPSVPAALPLLGELPRLLLLVLLCLPAVWG--DCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDS      ... ...ENST0000036706410Missing exon-YESMIS_120Missing exon ...Exon number: 1Exon region: chr1:130349072-130349035Nucleotide percent identity: 18.00 | BL ...

TOGA vs. hg38 (HLTOGAannotvHg38v1) Track Description
 

Description

TOGA (Tool to infer Orthologs from Genome Alignments) is a homology-based method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Methods

As input, TOGA uses a gene annotation of a reference species (human/hg38 for mammals, chicken/galGal6 for birds) and a whole genome alignment between the reference and query genome.

TOGA implements a novel paradigm that relies on alignments of intronic and intergenic regions and uses machine learning to accurately distinguish orthologs from paralogs or processed pseudogenes.

To annotate genes, CESAR 2.0 is used to determine the positions and boundaries of coding exons of a reference transcript in the orthologous genomic locus in the query species.

Display Conventions and Configuration

Each annotated transcript is shown in a color-coded classification as

  •   "intact": middle 80% of the CDS (coding sequence) is present and exhibits no gene-inactivating mutation. These transcripts likely encode functional proteins.
  •   "partially intact": 50% of the CDS is present in the query and the middle 80% of the CDS exhibits no inactivating mutation. These transcripts may also encode functional proteins, but the evidence is weaker as parts of the CDS are missing, often due to assembly gaps.
  •   "missing": <50% of the CDS is present in the query and the middle 80% of the CDS exhibits no inactivating mutation.
  •   "uncertain loss": there is 1 inactivating mutation in the middle 80% of the CDS, but evidence is not strong enough to classify the transcript as lost. These transcripts may or may not encode a functional protein.
  •   "lost": typically several inactivating mutations are present, thus there is strong evidence that the transcript is unlikely to encode a functional protein.

Clicking on a transcript provides additional information about the orthology classification, inactivating mutations, the protein sequence and protein/exon alignments.

Credits

This data was prepared by the Michael Hiller Lab

References

The TOGA software is available from github.com/hillerlab/TOGA

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales A, Ahmed AW, Kontopoulos DG, Hilgers L, Zoonomia Consortium, Hiller M. TOGA integrates gene annotation with orthology inference at scale. bioRxiv preprint September 2022