RetrogeneDB ID: retro_ptro_638

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:98629807..98630809(-)
• Located in intron of: ENSPTRG00000004204

Retrocopy information

• Ensembl ID: ENSPTRG00000039214
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSPTRG00000020317
• Aliases: None
• Description: COP9 signalosome subunit 5 [Source:HGNC Symbol;Acc:2240]

Sequence

>retro_ptro_638
ATGGTGGCGTCCGGGAGCGGTATGGCCCAGAAAACCTGGGAACTGGCCAACAACATGCAGGAAGCTCAGAGTATCGATGA
AATCTACAAATACGACAAGAAACAGCAGCAAGAAATCCTGGCGGCGAAGCCCTGGACTAAGGATCACCATTACTTTAAGT
ACTGCAAAATCTCAGCATTGGCTCTGCTGAAGATGGTGATGCATGCCAGATCGGGAGGCAACTTGGAAGTGATGGGTCTG
ATGCTAGGAAAGGTGGATGGTGAAACCATGATCATTATGGACAGTTTTGCTTTGCCTGTGGAGGGCACTGAAACCCGAGT
AAATGCTCAGGCTGCTGCATATGAATACATGGCTGCATACATAGAAAATGCGAAACAGGTTGGCCGCCTTGAAAATGCAA
TCGGGTGGTATCATAGCCACCCTGGCTATGGCTGCTGGCTTTCTGGGATTGATGTTAGTACTCAGATGCTCAATCAGCAG
TTCCAGGAACCATTTGTAGCAGTGGTGATTGATCCAACAAGAACAATATCCGCAGGGAAAGTGAATCTTGGCGCCTTTAG
GACATACCCAAAGGGCTACAAACCTCCTGATGAAGGACCTTCTGAGTACCAGACTATTCCACTTAATAAAATAGAAGATT
TTGGTGTACACTGCAAACAATATTATGCCTTAGAAGTCTCATATTTCAAATCCTCTTTGGATCGCAAATTGCTTGAGCTG
TTGTGGAATAAATACTGGGTGAATACGTTGAGTTCTTCTAGCTTGCTTACTAATGCAGACTATACCACTGGTCAGGTCTT
TGATTTGTCTGAAAAGTTAGAGCAGTCAGAAGCCCAGCTGGGACGAGGGAGTTTCATGTTGGGTTTAGAAACGCATGACC
GAAAATCAGAAGACAAACTTGCCAAAGCTACGAGAGACAGCTGTAAAACTACCATAGAAGCTATCCACGGATTGATGTCT
CAGGTTATTAAGGATAAACTGTTTAATCAAATTAACATCTCT

Alignment

ORF - retro_ptro_638 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHAR
          M.ASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHAR
Retrocopy MVASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHAR

Parental  SGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH
          SGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH
Retrocopy SGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH

Parental  PGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNK
          PGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNK
Retrocopy PGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNK

Parental  IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQL
          IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQL
Retrocopy IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQL

Parental  GRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
          GRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Retrocopy GRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS

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	0.93 RPM	22.90 RPM
SRP007412_cerebellum	0.00 RPM	6.35 RPM
SRP007412_heart	0.12 RPM	10.73 RPM
SRP007412_kidney	0.18 RPM	12.45 RPM
SRP007412_liver	0.16 RPM	6.51 RPM
SRP007412_testis	0.53 RPM	22.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_638 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Homo sapiens	ENSG00000121022	1 retrocopy	retro_hsap_3634,
Microcebus murinus	ENSMICG00000011042	1 retrocopy	retro_mmur_834,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Nomascus leucogenys	ENSNLEG00000010914	1 retrocopy	retro_nleu_815,
Pongo abelii	ENSPPYG00000018648	1 retrocopy	retro_pabe_2980,
Pan troglodytes	ENSPTRG00000020317	2 retrocopies	retro_ptro_2457, retro_ptro_638 ,