RetrogeneDB ID: retro_ptro_1176

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:39156674..39158233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TNPO1
• Ensembl ID: ENSPTRG00000016972
• Aliases: None
• Description: None

Sequence

>retro_ptro_1176
TCTGACTGGAATCTAAGGAAATGTTCTGTTGCCGCCCTAGATGTTCTTGCAAATGTGCATCATGATGAACTGCTGCCATA
TATATTGCCCCTTTTGAAAGAATTACTTTTTCATCATGAATGGGTTGTTAAAGAATTAGCCATCTTGGGTTTAGGAACAG
TTGCTGAAGGTTGCATGCAGGGCATGATTCCTTGCTTGCCTGAGCTTATTCCTCACCTTATTCAGTGCCTCTCTGATAAA
AAGGCTCTTGTCCGTTCCATAACATGCTGGACTCTTAGCCGCTATGCACACTGGGTAGTCAGCCAGCCACCAGACACGTA
CCTGAAGTCATTAATGACAGAGTTGCTAAAACGCATCCTGGATAGCAACAAGAGAGTACCAGAAGCTGCCTGCAGTGCCT
TTGCTACCCTAGAAGAGGAGGCTTGTACAGAACTTGTTGCTTACCTTGCTTATATACTTGATACCCTGGTCTTTGCATTT
AGTAAATACCAGCATAAGAACCTGCTCATTCTTTACAATGCCAGAGGGACATTAGCAGATTCAGTAGGACATCATTTAAA
CAAACCAGAATATATTCAAATGCTAATGCCTCCACTGATCCAGAAACGGAACATGTTAAAGGATGAAGATAAAGATCTTT
TCCCTTTACCTGAGTGTCCATTTTCAGCTACCACAGTGCTGCAGTCTGGCTTCCTTCCATACTGTGAACCTATGTGTCAG
CATTGGGTAAACCTAGTACAGAAGACTCTTGCACAAGCCATGCTAAGCAATGCTCAACCAGATCAATATGAAGCTCCAGA
TAAAGATTTTATGATAGTGGCTCTTGATTTACTGAGTGGCCTGGCTGAAGGACTTGGAGGCAATATTGAACAACTGGTAG
CCCGAAGTAACATCCTAACACTAACATATCAGTGCATGCAGGATAAAATGCCGGAAGTTCAACAGAGTTCTTTTGCCCTG
TTAAGTGACCTCACAAAAGCTTGCTTGCAGCATGTTAAGCCTTGTGTAGCTGATTTCATGCCAATATTGGGAACCAACCT
AACTCCAGAATTCATTTCAGTCTGCAACAATGACACATGAGCAATTGGAGAAATCCCCATTCAAATGGGTATAGAGATGC
AGCCTTATATCCCTATGGTGTTGCACCAGCTTGTAGAAATCATTAACAGACCCAACACACCAAAGACGTTGTTAAAGAAT
ACAGCAGTAACAATTGGTTGTCTTGGTTATGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTACGAGACCCTG
GTGCACCTCTCTGAGAAACATAAGACACAATGAGAAAAGGATTCAGCATTCCGTGGAATCTGCACCATGATCAGTGTGAA
TCCCAATGGCATAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATTATCTCAGAG
ACATGTTCTGTAAGATCCTTCATGGATTTAAAAATCAAATTGGCAATGAAAATGGGAGGCATTTCTCTGACCAGTTTCCT
CTTCCCTTAAAAGAGCATCTTGTAGCTTTTTATGGTGTT

Alignment

ORF - retro_ptro_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.21 %
• Parental protein coverage: 57.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELI
          SDWNLRKCS.AALDVLANV..DELLP.ILPLLKELLFHHEWVVKE..IL.LG..AEGCMQGMIP.LPELI
Retrocopy SDWNLRKCSVAALDVLANVHHDELLPYILPLLKELLFHHEWVVKELAILGLGTVAEGCMQGMIPCLPELI

Parental  PHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEE
          PHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLK.LMTELLKRILDSNKRV.EAACSAFATLEEE
Retrocopy PHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKSLMTELLKRILDSNKRVPEAACSAFATLEEE

Parental  ACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDED
          ACTELV.YLAYILDTLVFAFSKYQHKNLLILY.A.GTLADSVGHHLNKPEYIQMLMPPLIQK.NMLKDED
Retrocopy ACTELVAYLAYILDTLVFAFSKYQHKNLLILYNARGTLADSVGHHLNKPEYIQMLMPPLIQKRNMLKDED

Parental  KDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLSG
          KDLFPL.EC..S..T.LQSGFLPYCEP..Q..VNLVQKTLAQAML.NAQPDQYEAPDKDFMIVALDLLSG
Retrocopy KDLFPLPECPFSATTVLQSGFLPYCEPMCQHWVNLVQKTLAQAMLSNAQPDQYEAPDKDFMIVALDLLSG

Parental  LAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
          LAEGLGGNIEQLVARSNILTL.YQCMQDKMPEV.QSSFALL.DLTKAC.QHVKPC.ADFMPILGTNL.PE
Retrocopy LAEGLGGNIEQLVARSNILTLTYQCMQDKMPEVQQSSFALLSDLTKACLQHVKPCVADFMPILGTNLTPE

Parental  FISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAPML
          FISVCNN.T.AIGEI.IQMGIEMQPYIPMVLHQLVEIINRPNTPKTLL.NTA.TIG.LGYVCPQEVAPML
Retrocopy FISVCNNDT*AIGEIPIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLKNTAVTIGCLGYVCPQEVAPML

Parental  QQFIRPWCTSLRNIRDNE-EKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKILHG
          QQF.RPWCTSLRNIR.NE.EKDSAFRGICTMISVNP.G.IQDFIFFCDAVASWINPKD.LRDMFCKILHG
Retrocopy QQFTRPWCTSLRNIRHNE<EKDSAFRGICTMISVNPNGIIQDFIFFCDAVASWINPKDYLRDMFCKILHG

Parental  FKNQVGDENWRRFSDQFPLPLKERLAAFYGV
          FKNQ.G.EN.R.FSDQFPLPLKE.L.AFYGV
Retrocopy FKNQIGNENGRHFSDQFPLPLKEHLVAFYGV

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.70 RPM
SRP007412_cerebellum	0.00 RPM	64.31 RPM
SRP007412_heart	0.00 RPM	46.11 RPM
SRP007412_kidney	0.00 RPM	71.81 RPM
SRP007412_liver	0.00 RPM	27.43 RPM
SRP007412_testis	0.00 RPM	165.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1176 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000083312	2 retrocopies	retro_hsap_1724, retro_hsap_1813,
Mus musculus	ENSMUSG00000009470	1 retrocopy	retro_mmus_1501,
Pongo abelii	ENSPPYG00000015545	1 retrocopy	retro_pabe_1528,
Pan troglodytes	ENSPTRG00000016972	2 retrocopies	retro_ptro_1176 , retro_ptro_3060,
Tursiops truncatus	ENSTTRG00000000209	1 retrocopy	retro_ttru_1345,