Schema for LRG Regions - Locus Reference Genomic (LRG) Sequences Mapped to Dec. 2013 (GRCh38/hg38) Assembly
  Database: hg38    Primary Table: lrg Data last updated: 2019-10-26
Big Bed File: /gbdb/hg38/bbi/lrg.bb
Item Count: 919
Format description: Locus Reference Genomic regions
fieldexampledescription
chromchr1Reference assembly chromosome or scaffold
chromStart167428638Start position in chromosome
chromEnd167523609End position in chromosome
nameLRG_36LRG ID
score0Placeholder for BED format compatibility (0)
strand-Orientation of LRG to reference assembly: + or -
thickStart167428638Placeholder for BED format compatibility (same as chromStart)
thickEnd167523609Placeholder for BED format compatibility (same as chromEnd)
reserved0Placeholder for BED format compatibility (0)
blockCount1Number of gapless aligned blocks
blockSizes94971,Comma separated list of block sizes
chromStarts0,Start positions relative to chromStart
mismatches2086:92884:A:GList of bases that differ between LRG and reference assembly
indelsList of insertions/deletions in LRG and reference assembly
lrgSize94971Length in bases of LRG sequence
hgncId1677Numeric HGNC gene identifier
hgncSymbolCD247HGNC gene symbol
ncbiAccNG_007384.1NCBI accession of LRG sequence
lrgSourceCD247base: Mutation registry for Autosomal recessive CD3Zeta deficiencySource of LRG sequence
lrgSourceUrlhttp://structure.bmc.lu.se/idbase/CD247base/URL of lrgSource
creationDate2010-07-15Date on which this sequence was added as a LRG

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsmismatchesindelslrgSizehgncIdhgncSymbolncbiAcclrgSourcelrgSourceUrlcreationDate
chr1167428638167523609LRG_360-1674286381675236090194971,0,2086:92884:A:G949711677CD247NG_007384.1CD247base: Mutation registry for Autosomal recessive CD3Zeta deficiencyhttp://structure.bmc.lu.se/idbase/CD247base/2010-07-15
chr1169509953169591531LRG_5530-1695099531695915310181578,0,815783542F5NG_011806.1http://2015-08-12
chr1172654044172668873LRG_580+1726540441726688730114829,0,1482911936FASLGNG_007269.1FASLGbase: Mutation registry for Autoimmune lymphoproliferative syndrome, type 1B (ALPS1B) (previously known as TNFSF6base)http://structure.bmc.lu.se/idbase/FASLGbase/2010-09-24
chr1173901803173922378LRG_5770-1739018031739223780120575,0,20575775SERPINC1NG_012462.1http://2015-09-09
chr1179548538179580949LRG_8870-1795485381795809490132411,0,3241113394NPHS2NG_007535.1http://2015-07-01
chr1183553561183595581LRG_880-1835535611835955810142020,0,420207661NCF2NG_007267.1NCF2base: Mutation registry for autosomal recessive chronic granulomatous disease (CGD), deficiency of p67phoxhttp://structure.bmc.lu.se/idbase/NCF2base/2010-09-24
chr1193116957193256815LRG_5070+19311695719325681501139858,0,13985816783CDC73NG_012691.1http://2013-05-23
chr1196647010196749504LRG_470+19664701019674950401102494,0,60362:60362:T:C,74979:74979:A:T1024944883CFHNG_007259.1CFHbase: Mutation registry for Factor H deficiency (previously known as HF1base)http://structure.bmc.lu.se/idbase/CFHbase/2010-07-15
chr1196769799196796073LRG_1750+1967697991967960730126274,0,2627416980CFHR3NG_015993.1RAPID: Resource of Asian Primary Immunodeficiency Diseaseshttp://web16.kazusa.or.jp/rapid/browseByPIDGenes2011-04-12
chr1196814730196834189LRG_1490+1968147301968341890119459,0,194594888CFHR1NG_013060.1RAPID: Resource of Asian Primary Immunodeficiency Diseaseshttp://web16.kazusa.or.jp/rapid/browseByPIDGenes2011-04-12

LRG Regions (lrg) Track Description
 

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.

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