RetrogeneDB ID: retro_ptro_3060

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392673.1:3186..4751(-)
• 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_3060
ACAATTTCTGACTGGAATCTAAGGAAATGTTCTGTTGCTGCCCTAGATGTTCTTGCAAACGTGCATCATGATGAACTGCT
GCCATATATATTGCCCCTTTTGAAAGAATTACTTTTTCATCATGAATGGGTTGTTAAAGAATTAGCCATCTTGGGTTTAG
GAACAGTTGCTGAAGGTTGCATGCAGGGCATGATTCCTTGCTTGCCTGAGCTTATTCCTCACCTTATTCAGTGCCTCTCT
GATAAGAAGGCTCTTGTCCGTTCCATAACATGCTGGACTCTTAGCCGCTATGCACACTGGGTAGTCAGCCAGCCACCAGA
CACGTACCTGAAGTCATTAATGACAGAGTTGCTAAAACGCATCCTGGATAGCAACAAGAGAGTACCAGAAGCTGCCTGCA
GTGCCTTTGCTACCCTAGAAGAGGAGGCTTGTACAGAACTTGTTGCTTACCTTGCTTATATACTTGATACCCTGGTCTTT
GCATTTAGTAAATACCAGCATAAGAACCTGCTCATTCTTTACAATGCCAGAGGGACATTAGCAGATTCAGTAGGACATCA
TTTAAACAAACCAGAATATATTCAAATGCGAATGCCTCCACTGATCCAGAAACGGAACATGTTAAAGGATGAAGATAAAG
ATCTTTTCCCTTTACCTGAGTGTCCATTTTCAGCTGCCACAGTGCTGCAGTCTGGCTTCCTTCCACACTGTGAACCTATG
TGTCAGCATTGGGTAAACCTAGTACAGAAGACTCTTGCACAAGCCATGCTAAGCAGTGCTCAACCAGATCAATATGAAGC
TCCAGATAAAGATTTTATGATAGTGGCTCTTGATTTACTGAGTGGCCTGGCTGAAGGACTTGGAGGCAATATTGAACAAC
TGGTAGCCCGAAGTAACATCCTAACACTAACATATCAGTGCATGCAGGATAAAATGCCGGAAGTTCGACAGAGTTCTTTT
GCCCTGTTAAGTGACCTCACAAAAGCTTGCTTTCAGCATATTAAGGCTTGTGTAGCTGATTTCATGCCAATATTGGGAAC
CAACCTAACTGCAGAATTCATTTCAGTCTGCAACAATGACACATGAGCAATTGGAGAAATCCCCATTCAAATGGGTATAG
AGATGCAGCCTTATATCCCTATGGTGTTGCACCAGCTTGTAGAAATCATTAACAGACCCAACACACCAAAGACGTTGTTA
AAGAATACAGCAGTAACAATTGGTTGTCTTGGTTATGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTACGAG
ACCCTGGTGCACCTCTCTGAGAAACATAAGAGACAATGAGAAAAGGATTCAACATTCCGTGGAATCTGCATCATGATCAG
TGTGAATCCCAATGGCATAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATTATC
TCAGAGACATGTTCTGTAAGATCCTTCATGGATTTAAAAATCAAATTGGCAATGAAAATGGGAGGCATTTCTCTGACCAG
TTTCCTCTTCCCTTAAAAGAGCATCTTGTAGCTTTTTATGGTGTT

Alignment

ORF - retro_ptro_3060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.48 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TISDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPE
          TISDWNLRKCS.AALDVLANV..DELLP.ILPLLKELLFHHEWVVKE..IL.LG..AEGCMQGMIP.LPE
Retrocopy TISDWNLRKCSVAALDVLANVHHDELLPYILPLLKELLFHHEWVVKELAILGLGTVAEGCMQGMIPCLPE

Parental  LIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLE
          LIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLK.LMTELLKRILDSNKRV.EAACSAFATLE
Retrocopy LIPHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKSLMTELLKRILDSNKRVPEAACSAFATLE

Parental  EEACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKD
          EEACTELV.YLAYILDTLVFAFSKYQHKNLLILY.A.GTLADSVGHHLNKPEYIQM.MPPLIQK.NMLKD
Retrocopy EEACTELVAYLAYILDTLVFAFSKYQHKNLLILYNARGTLADSVGHHLNKPEYIQMRMPPLIQKRNMLKD

Parental  EDKDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLL
          EDKDLFPL.EC..S.AT.LQSGFLP.CEP..Q..VNLVQKTLAQAML..AQPDQYEAPDKDFMIVALDLL
Retrocopy EDKDLFPLPECPFSAATVLQSGFLPHCEPMCQHWVNLVQKTLAQAMLSSAQPDQYEAPDKDFMIVALDLL

Parental  SGLAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLN
          SGLAEGLGGNIEQLVARSNILTL.YQCMQDKMPEVRQSSFALL.DLTKACFQH.K.C.ADFMPILGTNL.
Retrocopy SGLAEGLGGNIEQLVARSNILTLTYQCMQDKMPEVRQSSFALLSDLTKACFQHIKACVADFMPILGTNLT

Parental  PEFISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAP
          .EFISVCNN.T.AIGEI.IQMGIEMQPYIPMVLHQLVEIINRPNTPKTLL.NTA.TIG.LGYVCPQEVAP
Retrocopy AEFISVCNNDT*AIGEIPIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLKNTAVTIGCLGYVCPQEVAP

Parental  MLQQFIRPWCTSLRNIRDNE-EKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKIL
          MLQQF.RPWCTSLRNIRDNE.EKDS.FRGIC.MISVNP.G.IQDFIFFCDAVASWINPKD.LRDMFCKIL
Retrocopy MLQQFTRPWCTSLRNIRDNE<EKDSTFRGICIMISVNPNGIIQDFIFFCDAVASWINPKDYLRDMFCKIL

Parental  HGFKNQVGDENWRRFSDQFPLPLKERLAAFYGV
          HGFKNQ.G.EN.R.FSDQFPLPLKE.L.AFYGV
Retrocopy HGFKNQIGNENGRHFSDQFPLPLKEHLVAFYGV

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	0.04 RPM	40.70 RPM
SRP007412_cerebellum	0.00 RPM	64.31 RPM
SRP007412_heart	0.00 RPM	46.11 RPM
SRP007412_kidney	0.03 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_3060 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3060 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,