What are the GRCh37/38 tRNA gene names
1
Hi all,
It may sound like a basic question but I'm straggling with finding the names of tRNA genes (but NOT the tRNA synthatases genes) as annotated in GRCh37/38 genome build. I basically want to search my gene list for tRNA genes but I cannot find the tRNA gene names. Note that HUGO gene names do not seem to be there in GRCh37/38. Can anyone help?
Thanks
gene
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Using mysql+ucsc?
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select * from knownGene as K,kgXref as X where X.kgId=K.name and X.geneSymbol like "TRNA%"\G'
*************************** 1. row ***************************
name: uc021pbo.1
chrom: chr1
strand: -
txStart: 159111400
txEnd: 159111474
cdsStart: 159111400
cdsEnd: 159111400
exonCount: 1
exonStarts: 159111400,
exonEnds: 159111474,
proteinID:
alignID: uc021pbo.1
kgID: uc021pbo.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AL035403.10/12461-12388
rfamAcc: RF00005
tRnaName:
*************************** 2. row ***************************
name: uc021qfa.1
chrom: chr11
strand: -
txStart: 20221785
txEnd: 20221851
cdsStart: 20221785
cdsEnd: 20221785
exonCount: 1
exonStarts: 20221785,
exonEnds: 20221851,
proteinID:
alignID: uc021qfa.1
kgID: uc021qfa.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AC068860.9/77170-77105
rfamAcc: RF00005
tRnaName:
*************************** 3. row ***************************
name: uc021qqe.1
chrom: chr11
strand: +
txStart: 109036041
txEnd: 109036120
cdsStart: 109036041
cdsEnd: 109036041
exonCount: 1
exonStarts: 109036041,
exonEnds: 109036120,
proteinID:
alignID: uc021qqe.1
kgID: uc021qqe.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AP003123.2/140474-140552
rfamAcc: RF00005
tRnaName:
*************************** 4. row ***************************
name: uc021qyx.1
chrom: chr12
strand: +
txStart: 56584147
txEnd: 56584229
cdsStart: 56584147
cdsEnd: 56584147
exonCount: 1
exonStarts: 56584147,
exonEnds: 56584229,
proteinID:
alignID: uc021qyx.1
kgID: uc021qyx.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AC073896.41/143418-143337
rfamAcc: RF00005
tRnaName:
*************************** 5. row ***************************
name: uc021rav.1
chrom: chr12
strand: +
txStart: 74851181
txEnd: 74851255
cdsStart: 74851181
cdsEnd: 74851181
exonCount: 1
exonStarts: 74851181,
exonEnds: 74851255,
proteinID:
alignID: uc021rav.1
kgID: uc021rav.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AC021648.25/58089-58016
rfamAcc: RF00005
tRnaName:
*************************** 6. row ***************************
name: uc021rjd.1
chrom: chr13
strand: -
txStart: 45492061
txEnd: 45492133
cdsStart: 45492061
cdsEnd: 45492061
exonCount: 1
exonStarts: 45492061,
exonEnds: 45492133,
proteinID:
alignID: uc021rjd.1
kgID: uc021rjd.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AL354816.5/99222-99151
rfamAcc: RF00005
tRnaName:
*************************** 7. row ***************************
name: uc021rlj.1
chrom: chr13
strand: -
txStart: 95201903
txEnd: 95201976
cdsStart: 95201903
cdsEnd: 95201903
exonCount: 1
exonStarts: 95201903,
exonEnds: 95201976,
proteinID:
alignID: uc021rlj.1
kgID: uc021rlj.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AL139318.9/123060-122988
rfamAcc: RF00005
tRnaName:
*************************** 8. row ***************************
name: uc021rqs.1
chrom: chr14
strand: +
txStart: 23398909
txEnd: 23398982
cdsStart: 23398909
cdsEnd: 23398909
exonCount: 1
exonStarts: 23398909,
exonEnds: 23398982,
proteinID:
alignID: uc021rqs.1
kgID: uc021rqs.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AL132780.5/33498-33570
rfamAcc: RF00005
tRnaName:
*************************** 9. row ***************************
name: uc021skk.1
chrom: chr15
strand: -
txStart: 45490803
txEnd: 45490875
cdsStart: 45490803
cdsEnd: 45490803
exonCount: 1
exonStarts: 45490803,
exonEnds: 45490875,
proteinID:
alignID: uc021skk.1
kgID: uc021skk.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AC051619.7/69973-69902
rfamAcc: RF00005
tRnaName:
*************************** 10. row ***************************
name: uc021skm.1
chrom: chr15
strand: -
txStart: 45492610
txEnd: 45492682
cdsStart: 45492610
cdsEnd: 45492610
exonCount: 1
exonStarts: 45492610,
exonEnds: 45492682,
proteinID:
alignID: uc021skm.1
kgID: uc021skm.1
mRNA:
spID:
spDisplayID:
geneSymbol: TRNA
refseq:
protAcc:
description: Rfam model RF00005 hit found at contig region AC051619.7/71780-71709
rfamAcc: RF00005
tRnaName:
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Hi Pierre,
Thank you for response.
Could you explain/clarify what is it that you taped/pasted ? I don't understand it. I haven't learn Pearl syntax (only Python and R).
it's a mysql command