This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What are the GRCh37/38 tRNA gene names

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
• 2,503 views • link
updated by Ram Ram • written by AlexAbdulkaderKheirallah AlexAbdulkaderKheirallah

1 answer

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:
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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).

• 0 views • link
updated by Ram Ram • written by AlexAbdulkaderKheirallah AlexAbdulkaderKheirallah

Log in to answer this question.

More posts like this