Schema for LRG Regions - Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly
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Database: hg38 Primary Table: lrg Data last updated: 2022-07-01
Big Bed File Download: /gbdb/hg38/bbi/lrg.bb Item Count: 1,459 The data is stored in the binary BigBed format.
Format description: Locus Reference Genomic regions
field | example | description |
chrom | chr1 | Reference assembly chromosome or scaffold | chromStart | 167428638 | Start position in chromosome | chromEnd | 167523609 | End position in chromosome | name | LRG_36 | LRG ID | score | 0 | Placeholder for BED format compatibility (0) | strand | - | Orientation of LRG to reference assembly: + or - | thickStart | 167428638 | Placeholder for BED format compatibility (same as chromStart) | thickEnd | 167523609 | Placeholder for BED format compatibility (same as chromEnd) | reserved | 0 | Placeholder for BED format compatibility (0) | blockCount | 1 | Number of gapless aligned blocks | blockSizes | 94971, | Comma separated list of block sizes | chromStarts | 0, | Start positions relative to chromStart | mismatches | 2086:92884:A:G | List of bases that differ between LRG and reference assembly | indels | | List of insertions/deletions in LRG and reference assembly | lrgSize | 94971 | Length in bases of LRG sequence | hgncId | 1677 | Numeric HGNC gene identifier | hgncSymbol | CD247 | HGNC gene symbol | ncbiAcc | NG_007384.1 | NCBI accession of LRG sequence | lrgSource | CD247base: Mutation registry for Autosomal recessive CD3Zeta deficiency | Source of LRG sequence | lrgSourceUrl | http://structure.bmc.lu.se/idbase/CD247base/ | URL of lrgSource | creationDate | 2010-07-15 | Date on which this sequence was added as a LRG |
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Sample Rows
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chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | mismatches | indels | lrgSize | hgncId | hgncSymbol | ncbiAcc | lrgSource | lrgSourceUrl | creationDate |
chr1 | 167428638 | 167523609 | LRG_36 | 0 | - | 167428638 | 167523609 | 0 | 1 | 94971, | 0, | 2086:92884:A:G | | 94971 | 1677 | CD247 | NG_007384.1 | CD247base: Mutation registry for Autosomal recessive CD3Zeta deficiency | http://structure.bmc.lu.se/idbase/CD247base/ | 2010-07-15 |
chr1 | 169509953 | 169591531 | LRG_553 | 0 | - | 169509953 | 169591531 | 0 | 1 | 81578, | 0, | | | 81578 | 3542 | F5 | NG_011806.1 | | http:// | 2015-08-12 |
chr1 | 172654044 | 172668873 | LRG_58 | 0 | + | 172654044 | 172668873 | 0 | 1 | 14829, | 0, | | | 14829 | 11936 | FASLG | NG_007269.1 | FASLGbase: Mutation registry for Autoimmune lymphoproliferative syndrome, type 1B (ALPS1B) (previously known as TNFSF6base) | http://structure.bmc.lu.se/idbase/FASLGbase/ | 2010-09-24 |
chr1 | 173819658 | 173860544 | LRG_1270 | 0 | + | 173819658 | 173860544 | 0 | 1 | 40886, | 0, | | | 40886 | 25538 | DARS2 | NG_016138.1 | | http:// | 2018-08-07 |
chr1 | 173901803 | 173922378 | LRG_577 | 0 | - | 173901803 | 173922378 | 0 | 1 | 20575, | 0, | | | 20575 | 775 | SERPINC1 | NG_012462.1 | | http:// | 2015-09-09 |
chr1 | 179548538 | 179580949 | LRG_887 | 0 | - | 179548538 | 179580949 | 0 | 1 | 32411, | 0, | | | 32411 | 13394 | NPHS2 | NG_007535.1 | | http:// | 2015-07-01 |
chr1 | 183553561 | 183595581 | LRG_88 | 0 | - | 183553561 | 183595581 | 0 | 1 | 42020, | 0, | | | 42020 | 7661 | NCF2 | NG_007267.1 | NCF2base: Mutation registry for autosomal recessive chronic granulomatous disease (CGD), deficiency of p67phox | http://structure.bmc.lu.se/idbase/NCF2base/ | 2010-09-24 |
chr1 | 186823899 | 186990981 | LRG_596 | 0 | + | 186823899 | 186990981 | 0 | 1 | 167082, | 0, | | | 167082 | 9035 | PLA2G4A | NG_012203.2 | | http:// | 2021-01-26 |
chr1 | 193116957 | 193256815 | LRG_507 | 0 | + | 193116957 | 193256815 | 0 | 1 | 139858, | 0, | | | 139858 | 16783 | CDC73 | NG_012691.1 | | http:// | 2013-05-23 |
chr1 | 196647010 | 196749504 | LRG_47 | 0 | + | 196647010 | 196749504 | 0 | 1 | 102494, | 0, | 60362:60362:T:C,74979:74979:A:T | | 102494 | 4883 | CFH | NG_007259.1 | CFHbase: Mutation registry for Factor H deficiency (previously known as HF1base) | http://structure.bmc.lu.se/idbase/CFHbase/ | 2010-07-15 |
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LRG Regions (lrg) Track Description
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Description
Locus Reference Genomic (LRG)
sequences are manually curated, stable DNA sequences that surround a
locus (typically a gene) and provide an unchanging coordinate system
for reporting sequence variants. They are not necessarily identical
to the corresponding sequence in a particular reference genome
assembly (such as Dec. 2013 (GRCh38/hg38)), but can be mapped to each version of a
reference genome assembly in order to convert between the stable LRG
variant coordinates and the various assembly coordinates.
We import the data from the LRG database at the EBI.
The NCBI RefSeqGene database is almost identical to LRG,
but it may contain a few more sequences. See the NCBI documentation.
Each LRG record also includes at least one stable transcript
on which variants may be reported. These transcripts
appear in the LRG Transcripts track in the Gene and Gene Predictions
track section.
Methods
LRG sequences are suggested by the community studying a locus (for example,
Locus-Specific Database curators, research laboratories, mutation consortia).
LRG curators then examine the submitted transcript as well as other known
transcripts at the locus, in the context of alignment and public expression
data.
For more information on the selection and annotation process, see the
LRG FAQ,
(Dalgleish, et al.) and (MacArthur, et al.).
Credits
This track was produced at UCSC using
LRG XML files.
Thanks to
LRG collaborators
for making these data available.
References
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P,
Vaughan BW et al.
Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
Genome Med. 2010 Apr 15;2(4):24.
PMID: 20398331; PMC: PMC2873802
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R,
Maglott DR et al.
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence
variants.
Nucleic Acids Res. 2014 Jan;42(Database issue):D873-8.
PMID: 24285302; PMC: PMC3965024
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