RetrogeneDB ID: retro_ptro_891

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:18620723..18621901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP10
• Ensembl ID: ENSPTRG00000008421
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:K7CR65]

Sequence

>retro_ptro_891
ATGGCCCTCCACAGCCCGCAGTATATTTTTGGAGATTTTAGTCCTGATGAATTCAATCAGTTCTTTGTGACTCCTCGATC
TTCAATTGAGCTTCCTCCATGCAGTGGAACAGTTCTGTGTGGCACACAAGCTGGGGATAAACTACCTGATGGACAAGAAT
ATCGGAGAATTGAGTTTGGTGTCAATGAAGTCATTGAACCCAGTGACAGTTTGCTGAGAACCCCCAGCTACAGTATTTCA
AGCACACTGAACCCTCAGGCCCCTGAATTTATTCTCGGTTGTACAGCTTCCAAAACAACCCCTGATGGTATCACTAAAGA
AGCAAGCTACGGCTCCATCGACTGCCAGTACCCAGGCTGTGCCCTTGCTTTGGATGGAAGTTCTAATGTGGAGGCGGAAG
TTTTGGAAAATGATGGTGTCTCAGGTGGTCTTGGACAAAGGGAGCGTAAAAAGAAGAAAAAGCAGCCACCTGGATATTAC
AGCTGTTTGAAAGATGGTGGCGATGATAGTATTTCCACAGAAGCCCTGGTCAATGGCCATGCCAACTCAGCAGTCCCTAA
CAGTGTCAGTGCAGAGGATGCAGAATTTATGGGTGACATGCCCCCGTCAGTTACGCCCAGGACTTTTGACAGCCCCCAGA
ACTCCACGGACTCTGTCAGTGACACTGTGCCTGACAGTCCCTTCCCCGGAGCACTCGGCAGTGACACCGGGACTGCAGGG
CAGCAGGAGGGGGGTCCCGGGGCTGATTTTGGTCAGTCCTGCTTCCCTGCAGGGGCTGGCAGAGACACCCTGTCAAGACA
GCTGGGGCTCAGCCCTGCGTTGGTACTGATACTACTGAAAACCTTGGAGTTGCTAATGGACAAATACTCGAATCCTCGGG
TGAGGGCACAGCTACCAACGGCGTGGAGTTGCACACCACGGAAAGCATAGACTTGGACCCAGCCAAACCCGAGAGTCCAT
CACCTCCTGCTGACGGCACGGGCTCTGCATCAGGCATCCTTCCTGTCAGCCAGCCCAGGTCCTGGGCCAGTCTCCTTCAC
GATTCTAAGCCCTCTTCCTCCTCGCCGGTGGCCTATGTGGAAACTAAGTATTCCCCTCCCGCCATATCTCCCCTGGTTTC
TGAAAAGCAGGTTGAAGTCAAAGAAGGGCTTGTTCCAGTTTCAGGGGATCCTGTAGCC

Alignment

ORF - retro_ptro_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.65 %
• Parental protein coverage: 50.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALHSPQYIFGDFSPDEFNQFFVTPRSSVELPPYSGTVLCGTQAVDKLPDGQEYQRIEFGVGEVIEPSDT
          MALHSPQYIFGDFSPDEFNQFFVTPRSS.ELPP.SGTVLCGTQA.DKLPDGQEY.RIEFGV.EVIEPSD.
Retrocopy MALHSPQYIFGDFSPDEFNQFFVTPRSSIELPPCSGTVLCGTQAGDKLPDGQEYRRIEFGVNEVIEPSDS

Parental  SPRTPSYSISSTLNPQAPEFILGCTASKITPDGITKEASYGSIDCQYPGSALALDGSSNVEAEVLESDGV
          ..RTPSYSISSTLNPQAPEFILGCTASK.TPDGITKEASYGSIDCQYPG.ALALDGSSNVEAEVLE.DGV
Retrocopy LLRTPSYSISSTLNPQAPEFILGCTASKTTPDGITKEASYGSIDCQYPGCALALDGSSNVEAEVLENDGV

Parental  SGGLGQRERKKKKKRPPGYYSYLKDGGDDSISTEALVNGHANSAVPNSVSAEDAEFMGDMPPSVTPRTCN
          SGGLGQRERKKKKK.PPGYYS.LKDGGDDSISTEALVNGHANSAVPNSVSAEDAEFMGDMPPSVTPRT..
Retrocopy SGGLGQRERKKKKKQPPGYYSCLKDGGDDSISTEALVNGHANSAVPNSVSAEDAEFMGDMPPSVTPRTFD

Parental  SPQNSTDSVSDIVPDSPFPGALGSDTRTAGQPEGGPGADFGQSCFPAEAGRDTLSR-TAGAQPCVGTDTT
          SPQNSTDSVSD.VPDSPFPGALGSDT.TAGQ.EGGPGADFGQSCFPA.AGRDTLSR.TAGAQPCVGTDTT
Retrocopy SPQNSTDSVSDTVPDSPFPGALGSDTGTAGQQEGGPGADFGQSCFPAGAGRDTLSR<TAGAQPCVGTDTT

Parental  ENLGVANGQILESSGEGTATNGVELHTTESIDLDPTKPESASPPADGTGSASGILPVSQPKSWASLFHDS
          ENLGVANGQILESSGEGTATNGVELHTTESIDLDP.KPES.SPPADGTGSASGILPVSQP.SWASL.HDS
Retrocopy ENLGVANGQILESSGEGTATNGVELHTTESIDLDPAKPESPSPPADGTGSASGILPVSQPRSWASLLHDS

Parental  KPSSSSPVAYVETKYSPPAISPLVSEKQVEVKEGLVPVSEDPVA
          KPSSSSPVAYVETKYSPPAISPLVSEKQVEVKEGLVPVS.DPVA
Retrocopy KPSSSSPVAYVETKYSPPAISPLVSEKQVEVKEGLVPVSGDPVA

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	27.96 RPM
SRP007412_cerebellum	0.00 RPM	52.41 RPM
SRP007412_heart	0.00 RPM	21.66 RPM
SRP007412_kidney	0.00 RPM	31.15 RPM
SRP007412_liver	0.03 RPM	25.43 RPM
SRP007412_testis	0.53 RPM	28.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_891 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009446	1 retrocopy	retro_btau_456,
Pan troglodytes	ENSPTRG00000008421	1 retrocopy	retro_ptro_891 ,