RetrogeneDB ID: retro_ptro_977

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:60886105..60886611(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX4I1
• Ensembl ID: ENSPTRG00000008434
• Aliases: None
• Description: Pan troglodytes cytochrome c oxidase subunit 4 isoform 1, mitochondrial (COX4I1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001251915]

Sequence

>retro_ptro_977
ATGTTGGCTACCAGGGTAGTTAGCCTAGTTGGCAAGCGAGCAATTTCCACCTTGGTGTCTGTACGAGCACACGGAAATGT
TGTGAAGAGCGATGACTATGCGCTCCCAGCTTATGTGGATCGACGTGACTATCCCGTACCCGATGTGGCCCATGTCAAGC
ACCTGTCTGCCAGACAGAAAGCCTTGAAGAAGAAGGAGAAGGCCTCCTGGAGCAACCGCTCCACGGATGGGAAAGTCGAG
TTGTATCACATTCAGTTCAAGGAGAGCTTTGCTGAGATGAACAGGGGCGTGAACGAGTGGAAGATGGTTGTGGGCGCTGC
CATGTTCTTCCTTGGCTTCACGGCGTTCATTATCATCTGGGAGAAGCGCTGTGTGTACGGCCCCATCCCGCACACCTTTG
ACAAAGAGTGGGTGCCCATGCAGACCAAGAGGATGCTGGACATGAGGTGAACCCCTGCAGGGCTTCGCCAGCCAAGTGGG
ACTATGACAAGAACGAGTGGAAGAAG

Alignment

ORF - retro_ptro_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASW
          MLATRV.SLVGKRAIST.V.VRAH..VVKS.D..LPAY.DRRD.P.P.VAHVKHLSA.QKALK.KEKASW
Retrocopy MLATRVVSLVGKRAISTLVSVRAHGNVVKSDDYALPAYVDRRDYPVPDVAHVKHLSARQKALKKKEKASW

Parental  SSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAK
          S..S.D.KVELY.I.FKESFAEMNRG.NEWK.VVG.AMFF.GFTA..I.W.K..VYGP.P..FDKEWV..
Retrocopy SNRSTDGKVELYHIQFKESFAEMNRGVNEWKMVVGAAMFFLGFTAFIIIWEKRCVYGPIPHTFDKEWVPM

Parental  QTKRMLDMK-VNPIQGLASKWDYEKNEWKK
          QTKRMLDM..VNP......KWDY.KNEWKK
Retrocopy QTKRMLDMR<VNPCRASPAKWDYDKNEWKK

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	0.23 RPM	304.63 RPM
SRP007412_cerebellum	0.07 RPM	210.32 RPM
SRP007412_heart	0.17 RPM	492.28 RPM
SRP007412_kidney	0.00 RPM	412.96 RPM
SRP007412_liver	0.00 RPM	255.95 RPM
SRP007412_testis	0.00 RPM	69.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_977 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_977 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_977 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1428
Gorilla gorilla	retro_ggor_1101
Pongo abelii	retro_pabe_1184
Macaca mulatta	retro_mmul_2260

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005479	1 retrocopy	retro_acar_90,
Ailuropoda melanoleuca	ENSAMEG00000018274	1 retrocopy	retro_amel_470,
Bos taurus	ENSBTAG00000016079	2 retrocopies	retro_btau_1406, retro_btau_483,
Canis familiaris	ENSCAFG00000019921	2 retrocopies	retro_cfam_1259, retro_cfam_1906,
Callithrix jacchus	ENSCJAG00000017319	4 retrocopies	retro_cjac_2267, retro_cjac_3264, retro_cjac_3300, retro_cjac_802,
Dasypus novemcinctus	ENSDNOG00000017207	3 retrocopies	retro_dnov_2207, retro_dnov_2396, retro_dnov_737,
Equus caballus	ENSECAG00000011722	1 retrocopy	retro_ecab_418,
Felis catus	ENSFCAG00000007612	2 retrocopies	retro_fcat_1484, retro_fcat_853,
Homo sapiens	ENSG00000131143	1 retrocopy	retro_hsap_1428,
Gorilla gorilla	ENSGGOG00000010047	1 retrocopy	retro_ggor_1101,
Loxodonta africana	ENSLAFG00000014002	1 retrocopy	retro_lafr_528,
Macaca mulatta	ENSMMUG00000006763	4 retrocopies	retro_mmul_1129, retro_mmul_1285, retro_mmul_1724, retro_mmul_2260,
Mus musculus	ENSMUSG00000031818	2 retrocopies	retro_mmus_1305, retro_mmus_2958,
Nomascus leucogenys	ENSNLEG00000011409	1 retrocopy	retro_nleu_1843,
Oryctolagus cuniculus	ENSOCUG00000001735	5 retrocopies	retro_ocun_1238, retro_ocun_1333, retro_ocun_317, retro_ocun_469, retro_ocun_889,
Ochotona princeps	ENSOPRG00000002129	4 retrocopies	retro_opri_1205, retro_opri_267, retro_opri_821, retro_opri_857,
Pongo abelii	ENSPPYG00000007619	3 retrocopies	retro_pabe_1183, retro_pabe_1184, retro_pabe_996,
Pan troglodytes	ENSPTRG00000008434	1 retrocopy	retro_ptro_977 ,
Rattus norvegicus	ENSRNOG00000017817	1 retrocopy	retro_rnor_1157,
Tarsius syrichta	ENSTSYG00000009682	2 retrocopies	retro_tsyr_2073, retro_tsyr_591,