RetrogeneDB ID: retro_pabe_1528

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:8432950..8434509(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TNPO1
• Ensembl ID: ENSPPYG00000015545
• Aliases: None
• Description: transportin-1 [Source:RefSeq peptide;Acc:NP_001125056]

Sequence

>retro_pabe_1528
TCTGACTGGAATCTAAGGAAGTGTTCTGTTGCTGCCCTAGATGTTCTTGCAAATGTGCATCATGATGAACTGCTGCCATA
TATATTGCCCCTTTTGAAAGAATTACTTTTTCATCATGAATGGGTTGTTAAAGAATCAGGCATCTTGGGTTTAGGAACAA
TTGCTGAAGGTTGCATGCAGGGCATGATGCCATACTTGCCTGAGCTTATTCCTCACCTTATTCAGTGCCTCTCTCATAAA
AAGGCTCTTGTCCATTCCATAACGTGCTGGACTCTTAGCCGCTATGCACACTGGGTAGTCAGCCAGCCACCAGACACGTA
CCTGAAGCCATTAATGACAGGATTGCTAAAGCGCATCCTGGATAGCAACAAGAGAGTACCAGAAGCTGCCTGCAGTGCCT
TTGCTACCCTAGAAGAGGAGGCTTGTACAGAACTTGTTCCTTACCTTGCTTATATACTTGATACCCTGGTCTTTGCATTT
AGTAAATACCAACATAAGAACCTGCTCATTCTTTACGATGCCAGAGGAACATCAGCGGATTCAGTAGGACATCATTTAAA
CAAACCAGAATATATTCAAATGCTAATGCCTCCACTGATCCAGAAATGGAACATGTTAAAGGATGAAGATAAAGATCTTT
TCCCTTTACCTGAGTGTCCATCTTCAGTTGCCACAGTGCTGCAGTCTGGCTTCCTTCCATACTGTGAAGCTGTGTATCAG
CATTGTGTAAACCTAGTACAGAAGACTCTTGCACAAGCCATGCTAAGCAATGCTCAACCAGATCAATATGAAGCTCCAGA
TAAAGATTTTATGATAGTGGCTCTTGATTTACTGAGTGGCCTGGCTGAAGGACTTGGAGGCAACATTGAACAGCTGGTAG
CCCGAAGTAACATCCTAACACTAACATATCAGTGCATGCAGGCTAAAATGCCGGAAGTTCGACAGAGTTCTTTTGCCCTG
TTAAGTGACCTCACAAAAGCTTGCTTTCAGCATGTTAAGCCTTGTGTAGCTGATTTCATGCCAATATTGGGAATCAACCT
AACTCCAGAATTCATTTCAGTCTGCAACAATGACACATGAGCAACTGGAGAAATCTCCATTCAAATGGGTATAGAGATGC
AGCCTTATATTCCTATGGTGTTGCACCAGCTTGTAGAAATCATTAATGGACCCAACACACCAAAGACGTTGTTAAAGAAT
TCAGCAATGGCAATTGGTCGTCTTGGTTATGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTACAAGACCCTG
GTGCACCTCTCTGAGAAACATAAGAGACAATAAGGAAAAGGATTCATCATTCCATGGAATTTGCACCATGATCAGTGTGA
ATCCCAATGGCATAATCCAAGATTTTATATTTTTTTGTGATGTTGTTGCATCATGGATTAACCCAAAAGATTATCTCAGA
GACATGTTCTGTAAGATCCTTCATGGATTTAAAAATCAAATTGGCGATGAAAATGGGAGGCATTTCTCTGACCAGTTTCC
TCTTCCCTTAAAAGAGCATCTTGCAGCTTTTATGGTGTT

Alignment

ORF - retro_pabe_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.17 %
• Parental protein coverage: 57.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDWNLRKCSAAALDVLANVYRDELLPHILPLLKELLFHHEWVVKESGILVLGAIAEGCMQGMIPYLPELI
          SDWNLRKCS.AALDVLANV..DELLP.ILPLLKELLFHHEWVVKESGIL.LG.IAEGCMQGM.PYLPELI
Retrocopy SDWNLRKCSVAALDVLANVHHDELLPYILPLLKELLFHHEWVVKESGILGLGTIAEGCMQGMMPYLPELI

Parental  PHLIQCLSDKKALVRSITCWTLSRYAHWVVSQPPDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEE
          PHLIQCLS.KKALV.SITCWTLSRYAHWVVSQPPDTYLKPLMT.LLKRILDSNKRV.EAACSAFATLEEE
Retrocopy PHLIQCLSHKKALVHSITCWTLSRYAHWVVSQPPDTYLKPLMTGLLKRILDSNKRVPEAACSAFATLEEE

Parental  ACTELVPYLAYILDTLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYIQMLMPPLIQKWNMLKDED
          ACTELVPYLAYILDTLVFAFSKYQHKNLLILYDA.GT.ADSVGHHLNKPEYIQMLMPPLIQKWNMLKDED
Retrocopy ACTELVPYLAYILDTLVFAFSKYQHKNLLILYDARGTSADSVGHHLNKPEYIQMLMPPLIQKWNMLKDED

Parental  KDLFPLLECLSSVATALQSGFLPYCEPVYQRCVNLVQKTLAQAMLNNAQPDQYEAPDKDFMIVALDLLSG
          KDLFPL.EC.SSVAT.LQSGFLPYCE.VYQ.CVNLVQKTLAQAML.NAQPDQYEAPDKDFMIVALDLLSG
Retrocopy KDLFPLPECPSSVATVLQSGFLPYCEAVYQHCVNLVQKTLAQAMLSNAQPDQYEAPDKDFMIVALDLLSG

Parental  LAEGLGGNIEQLVARSNILTLMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIADFMPILGTNLNPE
          LAEGLGGNIEQLVARSNILTL.YQCMQ.KMPEVRQSSFALL.DLTKACFQHVKPC.ADFMPILG.NL.PE
Retrocopy LAEGLGGNIEQLVARSNILTLTYQCMQAKMPEVRQSSFALLSDLTKACFQHVKPCVADFMPILGINLTPE

Parental  FISVCNNATWAIGEISIQMGIEMQPYIPMVLHQLVEIINRPNTPKTLLENTAITIGRLGYVCPQEVAPML
          FISVCNN.T.A.GEISIQMGIEMQPYIPMVLHQLVEIIN.PNTPKTLL.N.A..IGRLGYVCPQEVAPML
Retrocopy FISVCNNDT*ATGEISIQMGIEMQPYIPMVLHQLVEIINGPNTPKTLLKNSAMAIGRLGYVCPQEVAPML

Parental  QQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKILHGF
          QQF.RPWCTSLRNIRDN.EKDS.F.GICTMISVNP.G.IQDFIFFCD.VASWINPKD.LRDMFCKILHGF
Retrocopy QQFTRPWCTSLRNIRDNKEKDSSFHGICTMISVNPNGIIQDFIFFCDVVASWINPKDYLRDMFCKILHGF

Parental  KNQVGDENWRRFSDQFPLPLKERLAA-FYGV
          KNQ.GDEN.R.FSDQFPLPLKE.LAA.FYGV
Retrocopy KNQIGDENGRHFSDQFPLPLKEHLAA<FYGV

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	9.73 RPM
SRP007412_cerebellum	0.00 RPM	22.74 RPM
SRP007412_heart	0.00 RPM	13.79 RPM
SRP007412_kidney	0.00 RPM	16.01 RPM
SRP007412_liver	0.00 RPM	11.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1528 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1528 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,