RetrogeneDB ID: retro_ptro_44

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:56178732..56180868(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000021952
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSPTRG00000008891
• Aliases: None
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_ptro_44
ATGGCCCAGGTTCGAGAAACTTCTTTGCCCTCCGGCTCTGGGGTCCGCTGGATCTCCGGAGGTGGGGGAGGAGCCTCTCC
TGAGGAGGCGGTTGAGAAGGCGGGGAAAATGGAGGAGGCGGTGGCGGGGGCTACGAAGGCGTCTTCGAGACGGGAAGCTG
AGGAGATGAAGCTGGAGCCATTACAAGAGCGTGAGCCCGCGCCGGAGGAGAACTTGACGTGGAGCAGCAGCGGCGGCGAC
GAGAAGGTGCTCCCTTCAATCCCCCTTCGCTGTCACACCAGCTCCTCGCCCGTTTGCCCGCGCCGCAAGCCCCGCCCTCG
GCCCCAGCCCCGGGCCCGCTCCCGCAGCCAGCCTGGGCTCTCGGCCCCACCCCCGCCTCCAGCCCGGCCCCCGCCCCCGC
CGCCACCCCCGCCCCCACCCGCACCGCGGCCCAGGGCCTGGCGTGGATCCCGGCGCAGATCCCGGCCTGGGTCCAGGCCT
CAGACACGGAGAAGCTGCTCTGGTGACCTAGACGGGTCGGGGGATCCTGGCGGCTTAGGGGACTGGTTGCTGGAGGTCGA
GTTTGGTCAGGGTCCCACAGGCTGCTCTCATGTGGAGAGCTTTAAAGTAGGTAAGAACTGGCAGAAGAACCTGAGGTTGA
TCTACCAGCGTTTCGTTTGGAGTGGGACCCCAGAGACTAGGAAACGTAAAGCAAAGTCATGCATCTGTCACGTATGTAGT
ACCCATATGAACAGACTCCACTCTTGTCTCTCCTGTGTCTTTTTTGGCTGCTTCACTGAGAAACATATTCACAAACATGC
AGAAACAAAGCAGCACCATTTAGCTGTAGACCTTTATCATGGGGTCATATATTGCTTCATGTGTAAGGATTATGTATATG
ACAAAGACATAGAACAGATTGCCAAAGAAACAAAAGAAAAAATTTTGAGATTATTAACTTCCACCTCAACAGATGTTTCT
CATCAACAGTTTATGACATCAGGGTTTGAAGACAAGCAATCAACCTGTGAGACAAAGGAACAGGAGCCAAAATTGGTGAA
ACCCAAGAAAAAGAGAAGAAAAAAGTCAGTCTATACTGTAGGCCTGAGAGGGCTAATCAATCTTGGGAACACTTGTTTTA
TGAATTGTATTGTCCAGGCACTTACCCATATTCCTCTACTGAAAGATTTCTTCCTCTCTGACAAGCACAAATGTATAATG
ACAAGCCCCAGCTTGTGTCTGGTCTGTGAAATGTCTTCGCTTTTTCATGCTATGTACTCTGGGAGCCGAACTCCTCACAT
TCCCTATAAGTTACTGCATCTGATATGGATCCATGCAGAACATTTAGCAGGGTACAGGCAGCAGGATGCCCATGAGTTCC
TTATTGCAATATTAGACGTGCTACATAGACACAGCAAAGATGATAGTGGTGGGCAGGAGGCCAATAACCCCAACTGCTGT
AACTGCATCATAGACCAAATCTTTACAGGTGGCCTGCAATCAGATGTCACATGTCAAGCCTGCCATAGTGTTTCTACCAC
CATAGACCCATGCTGGGACATCAGTTTGGACTTGCCTGGCTCTTGTGCCACATTCGATTCCCAGAACCCAGAGAGGGCTG
ACAGCGCAGTGAGCAGGGATGACCACATACCAGGAATCCCCTCACTTACAGACTGTCTACAGTGGTTTACAAGGCCAGAG
CACCTAGGAAGCAGTGCCAAAATCAAATGCAATAGTTGCCAAAGCTACCAGGAGTCTACTAAACAGCTCACAATGAAAAA
ATTACCCATTGTGGCTTGTTTTCATCTCAAGCGGTTTGAGCATGTAGGCAAACAGAGGCGAAAGATTAATACCTTTATCT
CCTTTCCCTTGGAGCTGGACATGACTCCGTTTTTGGCCTCTACTAAAGAGAGCAGAATGAAAGAAGGCCAGCCACCAACA
GATTGTGTGCCCAATGAGAATAAGTATTCCTTGTTTGCAGTGATTAATCACCATGGAACTTTGGAAAGTGGCCACTATAC
CAGCTTCATCCGGCAACAAAAGGACCAGTGGTTCAGCTGTGATGATGCCATCATCACCAAGGCTACCATTGAGGACTTAC
TCTACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGGTCTAGAGAAAGACTAG

Alignment

ORF - retro_ptro_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.96 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPLLRDFFLSDRH
          G...K.ST.E....E..L.K...KRRK..S..T.GLRGLINLGNTCFMNCIVQALTH.PLL.DFFLSD.H
Retrocopy GFEDKQSTCETKEQEPKLVKPKKKRRK-KSVYTVGLRGLINLGNTCFMNCIVQALTHIPLLKDFFLSDKH

Parental  RCEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIAALDVLHRHCK
          .C.M.SPS.CLVCEMSSLF...YSG.R.PHIPYKLLHL.W.HA.HLAGY.QQDAHEFLIA.LDVLHRH.K
Retrocopy KCIMTSPSLCLVCEMSSLFHAMYSGSRTPHIPYKLLHLIWIHAEHLAGYRQQDAHEFLIAILDVLHRHSK

Parental  GDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFWPLSPGSEGNV
          .D..G..ANNPN.CNCIIDQIFTGGLQSDVTCQ.CH.VSTTIDP.WDISLDLPGS...F....P......
Retrocopy DDSGGQEANNPNCCNCIIDQIFTGGLQSDVTCQACHSVSTTIDPCWDISLDLPGSCATFDSQNPERADSA

Parental  VNGESHMSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHLKRFEHSAKLR
          V....H..G...LTDCL..FTRPEHLGSSAKIKC..C.SYQESTKQLTMKKLPIVACFHLKRFEH..K.R
Retrocopy VSRDDHIPGIPSLTDCLQWFTRPEHLGSSAKIKCNSCQSYQESTKQLTMKKLPIVACFHLKRFEHVGKQR

Parental  RKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLNNDNKYSLFAVVNHQGTLESGHYTSFIRQHKD
          RKI.T..SFPLELDMTPF.AS.KESRM....Q.PTD...N.NKYSLFAV.NH.GTLESGHYTSFIRQ.KD
Retrocopy RKINTFISFPLELDMTPFLASTKESRMK-EGQPPTDCVPNENKYSLFAVINHHGTLESGHYTSFIRQQKD

Parental  QWFKCDDAIITKASIKDVLDSEGYLLFYHKQFLE
          QWF.CDDAIITKA.I.D.L.SEGYLLFYHKQ.LE
Retrocopy QWFSCDDAIITKATIEDLLYSEGYLLFYHKQGLE

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	1.45 RPM	252.92 RPM
SRP007412_cerebellum	2.62 RPM	391.57 RPM
SRP007412_heart	0.79 RPM	106.97 RPM
SRP007412_kidney	3.79 RPM	193.76 RPM
SRP007412_liver	0.75 RPM	85.96 RPM
SRP007412_testis	1.58 RPM	57.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_44 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_44 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_44 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008978	1 retrocopy	retro_btau_82,
Canis familiaris	ENSCAFG00000018523	1 retrocopy	retro_cfam_125,
Homo sapiens	ENSG00000124422	1 retrocopy	retro_hsap_26,
Microcebus murinus	ENSMICG00000009998	1 retrocopy	retro_mmur_1,
Mus musculus	ENSMUSG00000042506	1 retrocopy	retro_mmus_239,
Otolemur garnettii	ENSOGAG00000015801	1 retrocopy	retro_ogar_274,
Pan troglodytes	ENSPTRG00000008891	1 retrocopy	retro_ptro_44 ,
Pteropus vampyrus	ENSPVAG00000001934	1 retrocopy	retro_pvam_905,
Ictidomys tridecemlineatus	ENSSTOG00000023814	1 retrocopy	retro_itri_163,