RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_591
TTGCTAAATCTTACTCCAAAGGGCAAGCAGGCTCCAGGGGGCCACGAGCTGAATTGTGACTTCTGGGGACTTATAGGGAT

GGCCCCTGCTGGAGGAGCAGATAACTTAATCAATGAAGTATCTGATGTCTATGTCCAGCTGAACAATAGGCATATGATGA

TCCGAGGAGAAAATATGTCCAAAATCCTAAAAGCACGTTCCATGATCACCAGGTGCTTCAGAGATCACTTCTTTGATAGG

GGGTACTGTGAAGTTACTCCTCCAATGTTGGTGCAGACACAGGTAGAAGGTGGTGCCACGCTCTTCAAGCTTGACTGTTT

CGGGGAAGAGGCATTTTTGACTCAGTCCTCTCAGTTGTACCTGGAGACCTGCCTTCCATCCTTGGGAGATGTTTTTTGTA

TTGCACAGTCATACAGAGCAGAACAATCCAGAACACGAAGTCACCTGGCTGAGTACACTCATGTGGAAGCTGAGTGCCCT

TTCCTGACCTTTTGAGGATCTCCTGAACAGATTGGAGGACTTGGTTTGTGAAGTGGTAGATAGAGTCTTAAAATCACTGG

CAGCAAGTATAGGGTATGACCTCAATCTGAACTTTAAACCCCCTAAACGGCCTTTCAAACAGATGAACTACTCTGATGCT

ATTGTGTGGCTAAAAGAACACAATGTAAAGAAAGAAGATGGGACTTTCTATGAATTTGGAGAAGATATCCCAGAAGCTCC

TGAGAGACTGATGACAGACACCATTAATGAACCAGTCTTGCTCTGTCGATTTCCTGTGAAGATCAAGTCCTTCTACATGC

AGCCATGTCCTGAGGATTCCCGCCTTACTGAATCTGTTGACGTGTTGATGCCCAATGTTGGTGAGATTGTGGGAGGCTCA

ATGCATATCTGGAATAGTGAAGAAATGCTGGCAGGTTATAAAAGGGAAGGGATTGACCCCACTCCTTACTGGTACACAGA

TCAGAGAAAATATGGTACACATCCTCATGGAGGATTCAGCTTGGGCTTAGAACGATTCCTGACTTGGATTCTGAATAGAT

ATCACACCCGAGATATATGCTTGTACCCGCAATTTGTCCAGCTCTGTAAGCCA

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:

                                ParentalMLNLTPKGKQAPGGHELSCDFWELMGLAPAGGADNLINEESDVDVQLNNRHMMIRGENMSKILKARSMIT
.LNLTPKGKQAPGGHEL.CDFW.L.G.APAGGADNLINE.SDV.VQLNNRHMMIRGENMSKILKARSMIT
RetrocopyLLNLTPKGKQAPGGHELNCDFWGLIGMAPAGGADNLINEVSDVYVQLNNRHMMIRGENMSKILKARSMIT
ParentalRCFRDHFFDRGYCEVTPPTLVQTQVEGGATLFKLDYFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA
RCFRDHFFDRGYCEVTPP.LVQTQVEGGATLFKLD.FGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA
RetrocopyRCFRDHFFDRGYCEVTPPMLVQTQVEGGATLFKLDCFGEEAFLTQSSQLYLETCLPSLGDVFCIAQSYRA
ParentalEQSRTRRHLAEYTHVEAECPFLT-FEDLLNRLEDLVCDVVDRVLKSPAASIVYDLNPNFKPPKRPFKRMN
EQSRTR.HLAEYTHVEAECPFLT.FEDLLNRLEDLVC.VVDRVLKS.AASI.YDLN.NFKPPKRPFK.MN
RetrocopyEQSRTRSHLAEYTHVEAECPFLT>FEDLLNRLEDLVCEVVDRVLKSLAASIGYDLNLNFKPPKRPFKQMN
ParentalYSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEPILLCRFPVEIKSFYMQRCPEDSRLTESV
YSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEP.LLCRFPV.IKSFYMQ.CPEDSRLTESV
RetrocopyYSDAIVWLKEHNVKKEDGTFYEFGEDIPEAPERLMTDTINEPVLLCRFPVKIKSFYMQPCPEDSRLTESV
ParentalDVLMPNVGEIVGGSMRIWDSEEILAGYKREGIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWILNRYH
DVLMPNVGEIVGGSM.IW.SEE.LAGYKREGIDPTP.YWYTDQRKYGT.PHGG..LGLERFLTWILNRYH
RetrocopyDVLMPNVGEIVGGSMHIWNSEEMLAGYKREGIDPTP-YWYTDQRKYGTHPHGGFSLGLERFLTWILNRYH
ParentalIRDVCLYPRFVQRCKP
.RD.CLYP.FVQ.CKP
RetrocopyTRDICLYPQFVQLCKP

                            

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

                        

RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_591 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_591 was not experimentally validated.

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.

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 ,

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

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

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

RetrogeneDB ID:

retro_itri_591