Schema for LRG Transcripts - Locus Reference Genomic (LRG) Fixed Transcript Annotations
  Database: hg38    Primary Table: lrgTranscriptAli    Row Count: 1,119   Data last updated: 2019-10-10
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 592smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 637int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 407int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName LRG_1231t1varchar(255) values Query sequence name
qSize 637int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 637int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 1013496int(10) unsigned range Alignment start position in target
tEnd 1014540int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 80,557,longblob   Size of each block
qStarts 0,80,longblob   Start of each block in query.
tStarts 1013496,1013983,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg38.lrgCdna.name (via lrgTranscriptAli.qName)
      hg38.lrgCds.id (via lrgTranscriptAli.qName)
      hg38.lrgPep.name (via lrgTranscriptAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
592637000001407+LRG_1231t16370637chr124895642210134961014540280,557,0,80,1013496,1013983,
97319000003528671+LRG_198t1731907319chr12489564221020122105611236251,262,48,216,225,225,207,219,195,201,149,106,117,165,144,125,106,339,138,128,115,120,354,193,216,230,135,97,165,112,117,193,88 ...0,251,513,561,777,1002,1227,1434,1653,1848,2049,2198,2304,2421,2586,2730,2855,2961,3300,3438,3566,3681,3801,4155,4348,4564,4794, ...1020122,1022200,1035276,1040664,1041172,1041477,1041955,1043238,1043537,1043822,1044108,1044333,1045160,1045358,1045732,1045963, ...
59410750000061739-LRG_1319t1107501075chr1248956422121133912141537286,129,197,67,102,123,171,0,286,415,612,679,781,904,1211339,1211703,1211941,1212637,1212991,1213662,1213982,
6344643000002020966-LRG_262t1464304643chr124895642264660916491700211481,762,200,116,133,120,138,150,111,150,51,96,189,204,152,137,92,61,106,130,64,0,1481,2243,2443,2559,2692,2812,2950,3100,3211,3361,3412,3508,3697,3901,4053,4190,4282,4343,4449,4579,6466091,6467824,6469041,6469334,6469543,6470235,6470505,6470734,6470989,6471487,6471757,6472526,6472985,6473250,6474012,6474450, ...
6521781000001115906-LRG_1165t1178101781chr12489564228860999887868612430,59,109,202,198,223,134,70,59,96,94,107,0,430,489,598,800,998,1221,1355,1425,1484,1580,1674,8860999,8862886,8863234,8863890,8865284,8866278,8867116,8867987,8870451,8871890,8874823,8878579,
825411000002371972+LRG_191t1541105411chr1248956422965173197291142471,105,173,229,230,180,150,90,222,97,131,51,168,122,144,100,179,113,79,168,124,146,133,2206,0,71,176,349,578,808,988,1138,1228,1450,1547,1678,1729,1897,2019,2163,2263,2442,2555,2634,2802,2926,3072,3205,9651731,9691466,9710423,9715540,9715848,9716439,9716958,9717536,9718693,9719920,9720111,9720610,9720741,9721126,9721443,9721760, ...
82105810000046160317+LRG_252t110581010581chr1248956422102107051038160347173,185,77,180,66,179,112,78,66,76,79,143,134,80,76,80,107,84,181,73,94,149,179,138,249,119,86,130,163,91,119,56,109,67,85,106,1 ...0,173,358,435,615,681,860,972,1050,1116,1192,1271,1414,1548,1628,1704,1784,1891,1975,2156,2229,2323,2472,2651,2789,3038,3157,324 ...10210705,10232249,10256246,10258492,10261904,10267379,10268151,10271501,10272240,10275427,10276320,10277985,10282399,10291081,10 ...
66942170000058654+LRG_659t1421704217chr124895642211012621110254926122,250,164,141,171,3369,0,122,372,536,677,848,11012621,11013715,11016843,11018732,11020428,11022123,
8387250000057147296-LRG_734t1872508725chr1248956422111065301126255158970,106,81,81,66,136,75,73,83,123,148,136,175,135,183,123,99,97,101,249,118,116,132,126,108,78,116,101,140,76,146,163,143,147,93 ...0,970,1076,1157,1238,1304,1440,1515,1588,1671,1794,1942,2078,2253,2388,2571,2694,2793,2890,2991,3240,3358,3474,3606,3732,3840,39 ...11106530,11108180,11109289,11109648,11112851,11114317,11114812,11115395,11117003,11121245,11121978,11124497,11126621,11127009,11 ...
847150000001113224-LRG_726t1715007150chr12489564221178572911806103125169,120,102,183,181,135,251,194,111,239,249,216,0,5169,5289,5391,5574,5755,5890,6141,6335,6446,6685,6934,11785729,11791206,11792277,11793906,11794357,11794728,11795097,11796205,11800211,11801160,11802880,11805887,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

LRG Transcripts (lrgTranscriptAli) Track Description
 

Description

This track shows the fixed (unchanging) transcript(s) associated with each Locus Reference Genomic (LRG) sequence. 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.

The LRG Regions track, in the Mapping and Sequencing Tracks section, includes more information about the LRG including the HGNC gene symbol for the gene at that locus, source of the LRG sequence, and summary of differences between LRG sequence and the genome assembly.

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