Schema for RefSeq mRNAs - RefSeq mRNAs mapped to this assembly |
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Database: hub_32_GCA_022605925.1 Primary Table: hub_32_xenoRefGene Data last updated: 2023-04-05
Big Bed File: https://hgdownload.soe.ucsc.edu/hubs/GCA/022/605/925/GCA_022605925.1/bbi/GCA_022605925.1_bLatJam1.0.a.xenoRefGene.bb
Item Count: 11,551
Format description: bigGenePred gene models
| field | example | description |
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| chrom | JAKCOY010000001.1 | Reference sequence chromosome or scaffold | | chromStart | 38279150 | Start position in chromosome | | chromEnd | 38410722 | End position in chromosome | | name | NM_028803.4 | RefSeq accession id | | score | 0 | Score (0-1000) | | strand | - | + or - for strand | | thickStart | 38279150 | Start of where display should be thick (start codon) | | thickEnd | 38410722 | End of where display should be thick (stop codon) | | reserved | 0 | RGB value (use R,G,B string in input file) | | blockCount | 15 | Number of blocks | | blockSizes | 45,120,48,183,170,113,4,96,133,123,205,91,133,117,69, | Comma separated list of block sizes | | chromStarts | 0,9581,25795,26924,62426,65014,67855,67869,71250,71636,97848,99198,101793,120799,131503, | Start positions relative to chromStart | | name2 | | Alternative/human readable name | | cdsStartStat | none | Status of CDS start annotation (none, unknown, incomplete, or complete) | | cdsEndStat | none | Status of CDS end annotation (none, unknown, incomplete, or complete) | | exonFrames | 0,0,0,0,1,2,1,1,0,0,2,1,0,0,0, | Exon frame {0,1,2}, or -1 if no frame for exon | | type | | Transcript type | | geneName | NM_028803.4 | gene name | | geneName2 | | species of origin of the mRNA | | geneType | | Gene type |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | name2 | cdsStartStat | cdsEndStat | exonFrames | type | geneName | geneName2 | geneType |
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| JAKCOY010000001.1 | 38279150 | 38410722 | NM_028803.4 | 0 | - | 38279150 | 38410722 | 0 | 15 | 45,120,48,183,170,113,4,96,133,123,205,91,133,117,69, | 0,9581,25795,26924,62426,65014,67855,67869,71250,71636,97848,99198,101793,120799,131503, | | none | none | 0,0,0,0,1,2,1,1,0,0,2,1,0,0,0, | | NM_028803.4 | | |
| JAKCOY010000001.1 | 39443250 | 39749474 | NM_019413.2 | 0 | + | 39443291 | 39747860 | 0 | 37 | 96,327,2,156,121,139,128,125,172,206,82,169,167,121,233,122,172,198,2,24,151,314,109,143,54,165,406,153,309,157,16,9,17,21,36,39 ... | 0,41946,42282,194383,221016,223827,224679,244012,245781,248499,250090,250324,250593,254347,256880,258358,261909,269274,269493,27 ... | | none | none | 0,1,1,0,0,1,2,1,0,1,0,1,2,1,2,1,0,1,1,0,0,1,0,1,0,0,0,1,1,1,2,-1,-1,-1,-1,-1,-1, | | NM_019413.2 | | |
| JAKCOY010000001.1 | 40039085 | 40197137 | NM_001378191.1 | 0 | - | 40041497 | 40197137 | 0 | 38 | 93,15,109,48,78,222,121,85,155,3,163,66,157,101,109,260,6,111,132,282,128,43,183,172,125,233,121,170,156,4,79,209,172,126,127,13 ... | 0,966,1308,1494,1802,1927,2189,2329,3503,8088,8114,8310,15619,30014,30124,33446,35025,40792,45376,45878,50227,51902,61197,67002, ... | | none | none | -1,-1,-1,-1,-1,-1,-1,1,2,2,1,1,0,1,0,1,1,1,1,1,2,1,1,0,1,2,1,2,2,1,0,1,0,0,2,1,0,0, | | NM_001378191.1 | | |
| JAKCOY010000001.1 | 40693504 | 40699270 | NM_174298.4 | 0 | + | 40693504 | 40699270 | 0 | 6 | 117,138,51,26,158,90, | 0,854,4991,5099,5498,5676, | | none | none | 0,0,0,0,2,1, | | NM_174298.4 | | |
| JAKCOY010000001.1 | 40748300 | 40765933 | NM_204737.1 | 0 | - | 40749018 | 40765927 | 0 | 11 | 84,169,72,36,102,36,170,59,4,534,130, | 0,117,298,426,550,662,709,1322,3824,4649,17503, | | none | none | -1,-1,-1,-1,-1,-1,1,2,1,1,0, | | NM_204737.1 | | |
| JAKCOY010000001.1 | 40937264 | 40948183 | NM_001126877.1 | 0 | + | 40937264 | 40948183 | 0 | 5 | 309,167,45,104,85, | 0,1076,4535,6635,10834, | | none | none | 0,0,2,2,1, | | NM_001126877.1 | | |
| JAKCOY010000001.1 | 40953749 | 41006961 | NM_174439.2 | 0 | - | 40953749 | 41006961 | 0 | 15 | 138,141,84,174,134,76,136,119,95,154,14,71,145,123,87, | 0,1812,2888,5270,15264,18074,20969,21561,22924,28674,29311,29343,31776,42643,53125, | | none | none | 2,2,2,2,0,2,1,2,0,2,0,1,0,0,0, | | NM_174439.2 | | |
| JAKCOY010000001.1 | 42193550 | 42483423 | NM_203409.1 | 0 | + | 42193581 | 42483423 | 0 | 21 | 76,75,3,210,138,137,29,157,146,150,188,87,175,5,117,120,177,9,200,121,111, | 0,157229,157322,158057,160512,165943,173179,178170,186740,201224,214674,216171,225394,235997,245792,248651,255367,255672,279235, ... | | none | none | 0,0,0,0,0,0,2,1,2,1,1,0,0,1,0,0,0,0,0,2,0, | | NM_203409.1 | | |
| JAKCOY010000001.1 | 44080206 | 44088680 | NM_001011362.1 | 0 | - | 44080206 | 44088680 | 0 | 7 | 51,153,105,65,100,138,141, | 0,931,4493,5927,7273,7861,8333, | | none | none | 0,0,0,1,0,0,0, | | NM_001011362.1 | | |
| JAKCOY010000001.1 | 44103836 | 44142193 | NM_001006257.1 | 0 | + | 44103859 | 44142045 | 0 | 8 | 76,66,113,206,102,108,32,181, | 0,23451,28377,31653,33333,35128,37054,38176, | | none | none | 0,2,2,1,0,0,0,2, | | NM_001006257.1 | | |
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RefSeq mRNAs (hub_32_xenoRefGene) Track Description
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Description
The RefSeq mRNAs gene track for the 17 Mar 2022 Laterallus jamaicensis coturniculus/GCA_022605925.1_bLatJam1.0.a
genome assembly displays translated blat alignments of vertebrate and
invertebrate mRNA in
GenBank.
Data Access
Download GCA_022605925.1_bLatJam1.0.a.xenoRefGene.gtf.gz GTF file.
Track statistics summary
Total genome size: 1,211,372,722
Gene count: 11,551
Bases in genes: 379,537,567
Percent genome coverage: % 31.331
Methods
The mRNAs were aligned against the Laterallus jamaicensis coturniculus/GCA_022605925.1_bLatJam1.0.a genome using
translated blat. When a single mRNA aligned in multiple places, the alignment
having the highest base identity was found. Only those alignments having a base
identity level within 1% of the best and at least 25% base identity with the
genomic sequence were kept.
Specifically, the translated blat command is:
blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl
where target.fa is one of the chromosome sequence of the genome assembly,
and the query.fa is the mRNAs from RefSeq
The resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25 -globalNearBest=0.0100 -minQSize=20
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
all.results.psl GCA_022605925.1_bLatJam1.0.a.xenoRefGene.psl
The filtered GCA_022605925.1_bLatJam1.0.a.xenoRefGene.psl is converted to
genePred data to display for this track.
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
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