DQ712113
 

Information on mRNA DQ712113

Description: Mus musculus piRNA piR-127435, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2006-06-08
Version: 1
mRNA sequence: DQ712113
Position: chr12:56960132-56960158

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    27  100.0%         12     -  56960132  56960158              DQ712113     1    27    27
browser |    27  100.0%          1     +   4627763   4627789              DQ712113     1    27    27
browser |    25  100.0%          1     -   7681950   7681974              DQ712113     1    25    27
browser |    27  100.0%          1     +   8728997   8729023              DQ712113     1    27    27
browser |    26  100.0%          1     -   8860120   8860145              DQ712113     1    26    27
browser |    27  100.0%          1     +  11100210  11100236              DQ712113     1    27    27
browser |    27  100.0%          1     +  11438153  11438179              DQ712113     1    27    27
browser |    26  100.0%          1     +  12017282  12017307              DQ712113     1    26    27
browser |    25  100.0%          1     -  14033241  14033265              DQ712113     1    25    27
browser |    27  100.0%          1     -  29697658  29697684              DQ712113     1    27    27
browser |    27  100.0%          1     +  30727293  30727319              DQ712113     1    27    27
browser |    27  100.0%          1     +  37318330  37318356              DQ712113     1    27    27
browser |    25  100.0%          1     -  41129770  41129794              DQ712113     1    25    27
browser |    27  100.0%          1     +  47263032  47263058              DQ712113     1    27    27
browser |    25  100.0%          1     -  47829586  47829610              DQ712113     1    25    27
browser |    26  100.0%          1     +  58789096  58789121              DQ712113     1    26    27
browser |    27  100.0%          1     -  76595417  76595443              DQ712113     1    27    27
browser |    27  100.0%          1     -  77648047  77648073              DQ712113     1    27    27
browser |    27  100.0%          1     -  95626920  95626946              DQ712113     1    27    27
browser |    27  100.0%          1     +  98528526  98528552              DQ712113     1    27    27
browser |    27  100.0%          1     + 108873423 108873449              DQ712113     1    27    27
browser |    27  100.0%          1     - 108887753 108887779              DQ712113     1    27    27
browser |    27  100.0%          1     - 111637734 111637760              DQ712113     1    27    27
browser |    26  100.0%          1     + 112192521 112192546              DQ712113     1    26    27
browser |    26  100.0%          1     - 112289957 112289982              DQ712113     1    26    27
browser |    27  100.0%          1     + 112492478 112492504              DQ712113     1    27    27
browser |    27  100.0%          1     + 117560416 117560442              DQ712113     1    27    27
browser |    27  100.0%          1     + 136736209 136736235              DQ712113     1    27    27
browser |    25  100.0%          1     + 146158380 146158404              DQ712113     1    25    27
browser |    27  100.0%          1     - 161363158 161363184              DQ712113     1    27    27
browser |    27  100.0%          1     - 166411727 166411753              DQ712113     1    27    27
browser |    27  100.0%          1     - 195009288 195009314              DQ712113     1    27    27
browser |    27  100.0%         10     +   3266786   3266812              DQ712113     1    27    27
browser |    26  100.0%         10     -   7193526   7193551              DQ712113     1    26    27
browser |    27  100.0%         10     -   8481680   8481706              DQ712113     1    27    27
browser |    27  100.0%         10     -   8513104   8513130              DQ712113     1    27    27
browser |    27  100.0%         10     -   9727063   9727089              DQ712113     1    27    27
browser |    27  100.0%         10     -  11576658  11576684              DQ712113     1    27    27
browser |    27  100.0%         10     +  11776999  11777025              DQ712113     1    27    27
browser |    27  100.0%         10     -  18117038  18117064              DQ712113     1    27    27
browser |    27  100.0%         10     -  19676795  19676821              DQ712113     1    27    27
browser |    26  100.0%         10     +  22399563  22399588              DQ712113     1    26    27
browser |    27  100.0%         10     +  23747667  23747693              DQ712113     1    27    27
browser |    27  100.0%         10     -  32814695  32814721              DQ712113     1    27    27
browser |    27  100.0%         10     +  34615431  34615458              DQ712113     1    27    27
browser |    27  100.0%         10     -  38469382  38469408              DQ712113     1    27    27
browser |    27  100.0%         10     -  43755542  43755568              DQ712113     1    27    27
browser |    27  100.0%         10     +  47512485  47512511              DQ712113     1    27    27
browser |    27  100.0%         10     -  47550214  47550240              DQ712113     1    27    27
browser |    27  100.0%         10     +  47557218  47557244              DQ712113     1    27    27
browser |    27  100.0%         10     +  48868465  48868491              DQ712113     1    27    27
browser |    26  100.0%         10     -  74714783  74714808              DQ712113     1    26    27
browser |    26  100.0%         10     -  76759201  76759226              DQ712113     1    26    27
browser |    26  100.0%         10     +  81506823  81506848              DQ712113     1    26    27
browser |    26  100.0%         10     +  81665951  81665976              DQ712113     1    26    27
browser |    27  100.0%         10     +  82407694  82407720              DQ712113     1    27    27
browser |    27  100.0%         10     -  86981163  86981189              DQ712113     1    27    27
browser |    27  100.0%         10     -  88493466  88493492              DQ712113     1    27    27
browser |    27  100.0%         10     +  97156869  97156895              DQ712113     1    27    27
browser |    27  100.0%         10     - 100419157 100419183              DQ712113     1    27    27
browser |    27  100.0%         10     - 103911925 103911951              DQ712113     1    27    27
browser |    27  100.0%         10     - 110536217 110536243              DQ712113     1    27    27
browser |    27  100.0%         10     - 121979036 121979062              DQ712113     1    27    27
browser |    27  100.0%         10     + 122669211 122669237              DQ712113     1    27    27
browser |    27  100.0%         11     -   6749679   6749705              DQ712113     1    27    27
browser |    27  100.0%         11     +   7526136   7526162              DQ712113     1    27    27
browser |    26  100.0%         11     +   9035239   9035264              DQ712113     1    26    27
browser |    27  100.0%         11     -  14521081  14521107              DQ712113     1    27    27
browser |    27  100.0%         11     +  14847093  14847119              DQ712113     1    27    27
browser |    27  100.0%         11     +  16154677  16154703              DQ712113     1    27    27
browser |    27  100.0%         11     -  16182198  16182224              DQ712113     1    27    27
browser |    27  100.0%         11     +  18756905  18756931              DQ712113     1    27    27
browser |    27  100.0%         11     +  19739174  19739200              DQ712113     1    27    27
browser |    27  100.0%         11     +  23193217  23193243              DQ712113     1    27    27
browser |    27  100.0%         11     -  27087658  27087684              DQ712113     1    27    27
browser |    27  100.0%         11     +  29114485  29114511              DQ712113     1    27    27
browser |    27  100.0%         11     -  29232570  29232596              DQ712113     1    27    27
browser |    27  100.0%         11     +  54467849  54467875              DQ712113     1    27    27
browser |    27  100.0%         11     +  70931650  70931676              DQ712113     1    27    27
browser |    27  100.0%         11     +  70957023  70957049              DQ712113     1    27    27
browser |    27  100.0%         11     +  73837536  73837562              DQ712113     1    27    27
browser |    27  100.0%         11     +  79632735  79632761              DQ712113     1    27    27
browser |    27  100.0%         11     -  79767432  79767458              DQ712113     1    27    27
browser |    26  100.0%         11     +  85330747  85330772              DQ712113     1    26    27
browser |    27  100.0%         11     -  90400754  90400780              DQ712113     1    27    27
browser |    26  100.0%         11     + 104750870 104750895              DQ712113     1    26    27
browser |    27  100.0%         12     +   3084165   3084191              DQ712113     1    27    27
browser |    27  100.0%         12     -   3112792   3112818              DQ712113     1    27    27
browser |    26  100.0%         12     -   6859681   6859706              DQ712113     1    26    27
browser |    25  100.0%         12     +  14644610  14644634              DQ712113     1    25    27
browser |    27  100.0%         12     -  18016463  18016489              DQ712113     1    27    27
browser |    27  100.0%         12     -  19831158  19831184              DQ712113     1    27    27
browser |    27  100.0%         12     +  19848804  19848830              DQ712113     1    27    27
browser |    27  100.0%         12     +  19864634  19864660              DQ712113     1    27    27
browser |    26  100.0%         12     -  21656468  21656493              DQ712113     1    26    27
browser |    27  100.0%         12     +  22425558  22425584              DQ712113     1    27    27
browser |    27  100.0%         12     +  23584570  23584596              DQ712113     1    27    27
browser |    27  100.0%         12     -  24745634  24745660              DQ712113     1    27    27
browser |    27  100.0%         12     +  26156919  26156945              DQ712113     1    27    27
browser |    26  100.0%         12     -  39485778  39485803              DQ712113     1    26    27
browser |    26  100.0%         12     +  52219990  52220015              DQ712113     1    26    27
browser |    27  100.0%         12     -  54407834  54407860              DQ712113     1    27    27
browser |    26  100.0%         12     +  60754132  60754157              DQ712113     1    26    27
browser |    27  100.0%         12     -  63338621  63338647              DQ712113     1    27    27
browser |    27  100.0%         12     -  74747343  74747369              DQ712113     1    27    27
browser |    27  100.0%         12     -  88482928  88482954              DQ712113     1    27    27
browser |    27  100.0%         12     -  90738017  90738043              DQ712113     1    27    27
browser |    27  100.0%         12     +  94235757  94235783              DQ712113     1    27    27
browser |    27  100.0%         12     -  96906700  96906726              DQ712113     1    27    27
browser |    27  100.0%         12     -  98328140  98328166              DQ712113     1    27    27
browser |    25  100.0%         12     - 105596460 105596484              DQ712113     2    26    27
browser |    27  100.0%         12     + 109787501 109787527              DQ712113     1    27    27
browser |    26  100.0%         13     -   3668373   3668398              DQ712113     1    26    27
browser |    27  100.0%         13     +   4510270   4510296              DQ712113     1    27    27
browser |    27  100.0%         13     +   4952151   4952177              DQ712113     1    27    27
browser |    27  100.0%         13     +   8317712   8317738              DQ712113     1    27    27
browser |    27  100.0%         13     -  12877976  12878002              DQ712113     1    27    27
browser |    27  100.0%         13     +  23823383  23823409              DQ712113     1    27    27
browser |    27  100.0%         13     -  27474254  27474280              DQ712113     1    27    27
browser |    26  100.0%         13     -  32489524  32489549              DQ712113     1    26    27
browser |    27  100.0%         13     -  32541180  32541206              DQ712113     1    27    27
browser |    26  100.0%         13     +  33958989  33959014              DQ712113     1    26    27
browser |    27  100.0%         13     +  50711575  50711601              DQ712113     1    27    27
browser |    26  100.0%         13     -  51189660  51189685              DQ712113     1    26    27
browser |    27  100.0%         13     -  54923217  54923243              DQ712113     1    27    27
browser |    26  100.0%         13     +  59269862  59269887              DQ712113     1    26    27
browser |    27  100.0%         13     +  61095335  61095361              DQ712113     1    27    27
browser |    27  100.0%         13     +  62807672  62807698              DQ712113     1    27    27
browser |    26  100.0%         13     +  64646865  64646890              DQ712113     1    26    27
browser |    26  100.0%         13     -  65668778  65668803              DQ712113     1    26    27
browser |    27  100.0%         13     -  68146439  68146465              DQ712113     1    27    27
browser |    27  100.0%         13     +  73291326  73291352              DQ712113     1    27    27
browser |    27  100.0%         13     +  81232317  81232343              DQ712113     1    27    27
browser |    27  100.0%         13     +  87212442  87212468              DQ712113     1    27    27
browser |    27  100.0%         13     +  88308789  88308815              DQ712113     1    27    27
browser |    26  100.0%         13     -  93674055  93674080              DQ712113     1    26    27
browser |    27  100.0%         13     - 102101160 102101186              DQ712113     1    27    27
browser |    26  100.0%         13     + 104084069 104084094              DQ712113     1    26    27
browser |    27  100.0%         13     - 106924244 106924270              DQ712113     1    27    27
browser |    27  100.0%         13     + 114675998 114676024              DQ712113     1    27    27
browser |    26  100.0%         14     +   5088202   5088227              DQ712113     1    26    27
browser |    26  100.0%         14     +   7002745   7002770              DQ712113     1    26    27
browser |    27  100.0%         14     +   8129954   8129980              DQ712113     1    27    27
browser |    27  100.0%         14     +  11143938  11143964              DQ712113     1    27    27
browser |    27  100.0%         14     -  13342144  13342170              DQ712113     1    27    27
browser |    27  100.0%         14     +  23022221  23022247              DQ712113     1    27    27
browser |    27  100.0%         14     -  29487745  29487771              DQ712113     1    27    27
browser |    27  100.0%         14     +  31641711  31641737              DQ712113     1    27    27
browser |    27  100.0%         14     +  37223073  37223099              DQ712113     1    27    27
browser |    26  100.0%         14     -  37749441  37749466              DQ712113     1    26    27
browser |    27  100.0%         14     -  39458725  39458751              DQ712113     1    27    27
browser |    27  100.0%         14     -  51559595  51559621              DQ712113     1    27    27
browser |    27  100.0%         14     -  53351244  53351270              DQ712113     1    27    27
browser |    26  100.0%         14     +  55464393  55464418              DQ712113     1    26    27
browser |    27  100.0%         14     +  60801989  60802015              DQ712113     1    27    27
browser |    27  100.0%         14     +  62880478  62880504              DQ712113     1    27    27
browser |    26  100.0%         14     -  65177365  65177390              DQ712113     1    26    27
browser |    27  100.0%         14     +  65416490  65416516              DQ712113     1    27    27
browser |    26  100.0%         14     -  66853941  66853966              DQ712113     1    26    27
browser |    27  100.0%         14     -  71459515  71459541              DQ712113     1    27    27
browser |    26  100.0%         14     -  72040934  72040959              DQ712113     1    26    27
browser |    27  100.0%         14     +  85415579  85415605              DQ712113     1    27    27
browser |    26  100.0%         14     -  86373034  86373059              DQ712113     1    26    27
browser |    27  100.0%         14     +  98992790  98992816              DQ712113     1    27    27
browser |    27  100.0%         14     - 101821046 101821072              DQ712113     1    27    27
browser |    27  100.0%         14     + 107063600 107063626              DQ712113     1    27    27
browser |    27  100.0%         14     + 117316806 117316832              DQ712113     1    27    27
browser |    27  100.0%         14     + 117523607 117523633              DQ712113     1    27    27
browser |    27  100.0%         14     + 121244948 121244974              DQ712113     1    27    27
browser |    27  100.0%         15     -   3199319   3199345              DQ712113     1    27    27
browser |    27  100.0%         15     -   5414489   5414515              DQ712113     1    27    27
browser |    27  100.0%         15     -  14731349  14731375              DQ712113     1    27    27
browser |    27  100.0%         15     -  16186040  16186066              DQ712113     1    27    27
browser |    27  100.0%         15     -  17581135  17581161              DQ712113     1    27    27
browser |    27  100.0%         15     -  19053338  19053364              DQ712113     1    27    27
browser |    27  100.0%         15     +  20155311  20155337              DQ712113     1    27    27
browser |    26  100.0%         15     +  22363168  22363193              DQ712113     1    26    27
browser |    27  100.0%         15     -  24325420  24325446              DQ712113     1    27    27
browser |    27  100.0%         15     +  27286687  27286713              DQ712113     1    27    27
browser |    27  100.0%         15     +  29131870  29131896              DQ712113     1    27    27
browser |    27  100.0%         15     +  39199516  39199542              DQ712113     1    27    27
browser |    27  100.0%         15     -  39581466  39581492              DQ712113     1    27    27
browser |    27  100.0%         15     -  46369625  46369651              DQ712113     1    27    27
browser |    27  100.0%         15     -  46770552  46770578              DQ712113     1    27    27
browser |    27  100.0%         15     -  51947607  51947633              DQ712113     1    27    27
browser |    27  100.0%         15     +  59034089  59034115              DQ712113     1    27    27
browser |    27  100.0%         15     -  60679606  60679632              DQ712113     1    27    27
browser |    27  100.0%         15     +  82489818  82489844              DQ712113     1    27    27
browser |    27  100.0%         15     -  93959745  93959771              DQ712113     1    27    27
browser |    27  100.0%         15     +  97448554  97448580              DQ712113     1    27    27
browser |    27  100.0%         16     +   7852325   7852351              DQ712113     1    27    27
browser |    26  100.0%         16     +   8882003   8882028              DQ712113     1    26    27
browser |    27  100.0%         16     +  13300003  13300029              DQ712113     1    27    27
browser |    27  100.0%         16     +  19407008  19407034              DQ712113     1    27    27
browser |    27  100.0%         16     +  20392065  20392091              DQ712113     1    27    27
browser |    26  100.0%         16     -  20927553  20927578              DQ712113     1    26    27
browser |    27  100.0%         16     -  22801372  22801398              DQ712113     1    27    27
browser |    27  100.0%         16     -  46944487  46944513              DQ712113     1    27    27
browser |    27  100.0%         16     -  51800097  51800123              DQ712113     1    27    27
browser |    27  100.0%         16     +  53400492  53400518              DQ712113     1    27    27
browser |    27  100.0%         16     +  54873512  54873538              DQ712113     1    27    27
browser |    27  100.0%         16     +  58156590  58156616              DQ712113     1    27    27
browser |    27  100.0%         16     +  61133369  61133395              DQ712113     1    27    27
browser |    26  100.0%         16     +  61145009  61145034              DQ712113     1    26    27
browser |    26  100.0%         16     +  61151026  61151051              DQ712113     1    26    27
browser |    27  100.0%         16     +  62199272  62199298              DQ712113     1    27    27
browser |    27  100.0%         16     -  64790424  64790450              DQ712113     1    27    27
browser |    26  100.0%         16     -  69762390  69762415              DQ712113     1    26    27
browser |    27  100.0%         16     +  70068138  70068164              DQ712113     1    27    27
browser |    27  100.0%         16     +  71816733  71816759              DQ712113     1    27    27
browser |    27  100.0%         16     +  78242140  78242166              DQ712113     1    27    27
browser |    27  100.0%         16     +  79339740  79339766              DQ712113     1    27    27
browser |    27  100.0%         16     -  88946219  88946245              DQ712113     1    27    27
browser |    27  100.0%         16     -  97904257  97904283              DQ712113     1    27    27
browser |    27  100.0%         17     -  15091323  15091349              DQ712113     1    27    27
browser |    27  100.0%         17     +  23338627  23338653              DQ712113     1    27    27
browser |    27  100.0%         17     -  34451450  34451476              DQ712113     1    27    27
browser |    26  100.0%         17     -  50227644  50227669              DQ712113     1    26    27
browser |    26  100.0%         17     -  52257659  52257684              DQ712113     1    26    27
browser |    27  100.0%         17     -  52635571  52635597              DQ712113     1    27    27
browser |    27  100.0%         17     -  53678497  53678523              DQ712113     1    27    27
browser |    27  100.0%         17     +  60612294  60612320              DQ712113     1    27    27
browser |    27  100.0%         17     +  66834505  66834531              DQ712113     1    27    27
browser |    26  100.0%         17     -  67736502  67736527              DQ712113     1    26    27
browser |    27  100.0%         17     -  72763131  72763157              DQ712113     1    27    27
browser |    27  100.0%         17     +  72882462  72882488              DQ712113     1    27    27
browser |    27  100.0%         17     +  74163578  74163604              DQ712113     1    27    27
browser |    27  100.0%         17     -  78232289  78232315              DQ712113     1    27    27
browser |    27  100.0%         17     +  78778612  78778638              DQ712113     1    27    27
browser |    27  100.0%         17     +  92556837  92556863              DQ712113     1    27    27
browser |    27  100.0%         17     +  94099345  94099371              DQ712113     1    27    27
browser |    27  100.0%         18     +   4480026   4480052              DQ712113     1    27    27
browser |    27  100.0%         18     +   5110207   5110233              DQ712113     1    27    27
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browser |    27  100.0%          9     +  18927346  18927372              DQ712113     1    27    27
browser |    27  100.0%          9     +  18957894  18957920              DQ712113     1    27    27
browser |    27  100.0%          9     -  19816724  19816750              DQ712113     1    27    27
browser |    26  100.0%          9     +  19867115  19867140              DQ712113     1    26    27
browser |    26  100.0%          9     +  22089208  22089233              DQ712113     1    26    27
browser |    27  100.0%          9     +  31990698  31990724              DQ712113     1    27    27
browser |    26  100.0%          9     +  53924158  53924183              DQ712113     1    26    27
browser |    26  100.0%          9     +  79940449  79940474              DQ712113     1    26    27
browser |    27  100.0%          9     -  82661891  82661917              DQ712113     1    27    27
browser |    27  100.0%          9     +  85799144  85799170              DQ712113     1    27    27
browser |    27  100.0%          9     +  92288641  92288667              DQ712113     1    27    27
browser |    27  100.0%          9     +  98333891  98333917              DQ712113     1    27    27
browser |    27  100.0%          9     - 109299798 109299824              DQ712113     1    27    27
browser |    27  100.0%          9     + 113055690 113055716              DQ712113     1    27    27
browser |    27  100.0%          9     - 114707530 114707556              DQ712113     1    27    27
browser |    27  100.0%          9     - 114803249 114803275              DQ712113     1    27    27
browser |    27  100.0%          9     - 117973311 117973337              DQ712113     1    27    27
browser |    26  100.0%          9     - 118039871 118039896              DQ712113     1    26    27
browser |    27  100.0%          9     - 119704309 119704335              DQ712113     1    27    27
browser |    26  100.0%          X     -   9254719   9254744              DQ712113     1    26    27
browser |    26  100.0%          X     +  15522916  15522941              DQ712113     1    26    27
browser |    27  100.0%          X     +  19492901  19492927              DQ712113     1    27    27
browser |    27  100.0%          X     +  35179087  35179113              DQ712113     1    27    27
browser |    27  100.0%          X     +  42916764  42916790              DQ712113     1    27    27
browser |    27  100.0%          X     +  49503421  49503447              DQ712113     1    27    27
browser |    27  100.0%          X     +  62619571  62619597              DQ712113     1    27    27
browser |    27  100.0%          X     -  65829222  65829248              DQ712113     1    27    27
browser |    27  100.0%          X     -  70731262  70731288              DQ712113     1    27    27
browser |    27  100.0%          X     +  70924203  70924229              DQ712113     1    27    27
browser |    27  100.0%          X     +  77381885  77381911              DQ712113     1    27    27
browser |    27  100.0%          X     +  79601873  79601899              DQ712113     1    27    27
browser |    27  100.0%          X     +  80883492  80883518              DQ712113     1    27    27
browser |    27  100.0%          X     +  83552641  83552667              DQ712113     1    27    27
browser |    27  100.0%          X     +  88564611  88564637              DQ712113     1    27    27
browser |    27  100.0%          X     -  88724943  88724969              DQ712113     1    27    27
browser |    27  100.0%          X     -  96230493  96230519              DQ712113     1    27    27
browser |    27  100.0%          X     +  96801965  96801991              DQ712113     1    27    27
browser |    27  100.0%          X     + 105734941 105734967              DQ712113     1    27    27
browser |    27  100.0%          X     + 110048542 110048568              DQ712113     1    27    27
browser |    27  100.0%          X     + 113800131 113800157              DQ712113     1    27    27
browser |    27  100.0%          X     - 115565538 115565564              DQ712113     1    27    27
browser |    26  100.0%          X     - 116388634 116388659              DQ712113     1    26    27
browser |    27  100.0%          X     + 120460258 120460284              DQ712113     1    27    27
browser |    27  100.0%          X     - 124963705 124963731              DQ712113     1    27    27
browser |    27  100.0%          X     + 125259154 125259180              DQ712113     1    27    27
browser |    27  100.0%          X     + 130242773 130242799              DQ712113     1    27    27
browser |    27  100.0%          X     - 132125406 132125432              DQ712113     1    27    27
browser |    27  100.0%          X     + 141953517 141953543              DQ712113     1    27    27
browser |    27  100.0%          X     + 145479992 145480018              DQ712113     1    27    27
browser |    27  100.0%          X     + 151352613 151352639              DQ712113     1    27    27
browser |    27  100.0%          X     - 161107303 161107329              DQ712113     1    27    27
browser |    27  100.0%          X     - 164656553 164656579              DQ712113     1    27    27
browser |    27  100.0%          X     - 166964022 166964048              DQ712113     1    27    27
browser |    27  100.0%  X_GL456233v2_random     -    498637    498663              DQ712113     1    27    27
browser |    26  100.0%          Y     +    986086    986111              DQ712113     1    26    27
browser |    26  100.0%          Y     -   5508731   5508756              DQ712113     1    26    27
browser |    26  100.0%          Y     -   6772690   6772715              DQ712113     1    26    27
browser |    26  100.0%          Y     -  15359418  15359443              DQ712113     1    26    27
browser |    26  100.0%          Y     -  20071939  20071964              DQ712113     1    26    27
browser |    27  100.0%          Y     +  21873767  21873793              DQ712113     1    27    27
browser |    27  100.0%          Y     +  23481259  23481285              DQ712113     1    27    27
browser |    27  100.0%          Y     -  35057014  35057040              DQ712113     1    27    27
browser |    27  100.0%          Y     +  35703844  35703870              DQ712113     1    27    27
browser |    26  100.0%          Y     +  39959779  39959804              DQ712113     1    26    27
browser |    26  100.0%          Y     +  42326376  42326401              DQ712113     1    26    27
browser |    26  100.0%          Y     -  46191024  46191049              DQ712113     1    26    27
browser |    26  100.0%          Y     +  46435862  46435887              DQ712113     1    26    27
browser |    27  100.0%          Y     +  53870717  53870743              DQ712113     1    27    27
browser |    26  100.0%          Y     +  59353806  59353831              DQ712113     1    26    27
browser |    27  100.0%          Y     +  69399211  69399237              DQ712113     1    27    27
browser |    27  100.0%          Y     +  69686116  69686142              DQ712113     1    27    27
browser |    27  100.0%          Y     +  73710747  73710773              DQ712113     1    27    27
browser |    27  100.0%          Y     -  81110803  81110829              DQ712113     1    27    27
browser |    27  100.0%          Y     +  82266681  82266707              DQ712113     1    27    27

View details of parts of alignment within browser window
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Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518