RetrogeneDB ID: retro_itri_591

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393304.1:12615609..12616702(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000029091
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NARS
• Ensembl ID: ENSSTOG00000002118
• Aliases: None
• Description: asparaginyl-tRNA synthetase [Source:HGNC Symbol;Acc:7643]

Sequence

>retro_itri_591
TTGCTAAATCTTACTCCAAAGGGCAAGCAGGCTCCAGGGGGCCACGAGCTGAATTGTGACTTCTGGGGACTTATAGGGAT
GGCCCCTGCTGGAGGAGCAGATAACTTAATCAATGAAGTATCTGATGTCTATGTCCAGCTGAACAATAGGCATATGATGA
TCCGAGGAGAAAATATGTCCAAAATCCTAAAAGCACGTTCCATGATCACCAGGTGCTTCAGAGATCACTTCTTTGATAGG
GGGTACTGTGAAGTTACTCCTCCAATGTTGGTGCAGACACAGGTAGAAGGTGGTGCCACGCTCTTCAAGCTTGACTGTTT
CGGGGAAGAGGCATTTTTGACTCAGTCCTCTCAGTTGTACCTGGAGACCTGCCTTCCATCCTTGGGAGATGTTTTTTGTA
TTGCACAGTCATACAGAGCAGAACAATCCAGAACACGAAGTCACCTGGCTGAGTACACTCATGTGGAAGCTGAGTGCCCT
TTCCTGACCTTTTGAGGATCTCCTGAACAGATTGGAGGACTTGGTTTGTGAAGTGGTAGATAGAGTCTTAAAATCACTGG
CAGCAAGTATAGGGTATGACCTCAATCTGAACTTTAAACCCCCTAAACGGCCTTTCAAACAGATGAACTACTCTGATGCT
ATTGTGTGGCTAAAAGAACACAATGTAAAGAAAGAAGATGGGACTTTCTATGAATTTGGAGAAGATATCCCAGAAGCTCC
TGAGAGACTGATGACAGACACCATTAATGAACCAGTCTTGCTCTGTCGATTTCCTGTGAAGATCAAGTCCTTCTACATGC
AGCCATGTCCTGAGGATTCCCGCCTTACTGAATCTGTTGACGTGTTGATGCCCAATGTTGGTGAGATTGTGGGAGGCTCA
ATGCATATCTGGAATAGTGAAGAAATGCTGGCAGGTTATAAAAGGGAAGGGATTGACCCCACTCCTTACTGGTACACAGA
TCAGAGAAAATATGGTACACATCCTCATGGAGGATTCAGCTTGGGCTTAGAACGATTCCTGACTTGGATTCTGAATAGAT
ATCACACCCGAGATATATGCTTGTACCCGCAATTTGTCCAGCTCTGTAAGCCA

Alignment

ORF - retro_itri_591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 65.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLNLTPKGKQAPGGHELSCDFWELMGLAPAGGADNLINEESDVDVQLNNRHMMIRGENMSKILKARSMIT
          .LNLTPKGKQAPGGHEL.CDFW.L.G.APAGGADNLINE.SDV.VQLNNRHMMIRGENMSKILKARSMIT
Retrocopy LLNLTPKGKQAPGGHELNCDFWGLIGMAPAGGADNLINEVSDVYVQLNNRHMMIRGENMSKILKARSMIT

Parental  RCFRDHFFDRGYCEVTPPTLVQTQVEGGATLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA
          RCFRDHFFDRGYCEVTPP.LVQTQVEGGATLFKLD.FGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA
Retrocopy RCFRDHFFDRGYCEVTPPMLVQTQVEGGATLFKLDCFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA

Parental  EQSRTRRHLAEYTHVEAECPFLT-FEDLLNRLEDLVCDVVDRVLKSPAASIVYDLNPNFKPPKRPFKRMN
          EQSRTR.HLAEYTHVEAECPFLT.FEDLLNRLEDLVC.VVDRVLKS.AASI.YDLN.NFKPPKRPFK.MN
Retrocopy EQSRTRSHLAEYTHVEAECPFLT>FEDLLNRLEDLVCEVVDRVLKSLAASIGYDLNLNFKPPKRPFKQMN

Parental  YSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEPILLCRFPVEIKSFYMQRCPEDSRLTESV
          YSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEP.LLCRFPV.IKSFYMQ.CPEDSRLTESV
Retrocopy YSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEPVLLCRFPVKIKSFYMQPCPEDSRLTESV

Parental  DVLMPNVGEIVGGSMRIWDSEEILAGYKREGIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWILNRYH
          DVLMPNVGEIVGGSM.IW.SEE.LAGYKREGIDPTP.YWYTDQRKYGT.PHGG..LGLERFLTWILNRYH
Retrocopy DVLMPNVGEIVGGSMHIWNSEEMLAGYKREGIDPTP-YWYTDQRKYGTHPHGGFSLGLERFLTWILNRYH

Parental  IRDVCLYPRFVQRCKP
          .RD.CLYP.FVQ.CKP
Retrocopy TRDICLYPQFVQLCKP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_591 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_591 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003837	2 retrocopies	retro_cjac_2194, retro_cjac_3091,
Cavia porcellus	ENSCPOG00000013227	3 retrocopies	retro_cpor_1441, retro_cpor_429, retro_cpor_736,
Loxodonta africana	ENSLAFG00000000559	1 retrocopy	retro_lafr_955,
Macropus eugenii	ENSMEUG00000000774	1 retrocopy	retro_meug_2019,
Otolemur garnettii	ENSOGAG00000016302	1 retrocopy	retro_ogar_1061,
Ictidomys tridecemlineatus	ENSSTOG00000002118	1 retrocopy	retro_itri_591 ,