RetrogeneDB ID: retro_ptro_422

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:43603440..43603713(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRHL
• Ensembl ID: ENSPTRG00000000691
• Aliases: None
• Description: Cytochrome b-c1 complex subunit 6 [Source:UniProtKB/TrEMBL;Acc:H2PYY7]

Sequence

>retro_ptro_422
ATGGGACTGGAGGATGAGCAAAAGATGCTGAGCAGGTCCTGAGATCCTAAGGAGGAGGAAGAGGAAGAGGAGGAATGAGT
GAATCCCCTAACAACCGTGAGATAGCAATGCGAGCAGTTGGAGAAATGTGTAAAGGCCTGGAAGCAGCTAGAGCTCTGTG
ACAAGTGTGTTATCCTCTCGATCACATACAGAAGAGGATTGCAAGAGGAGCTCTTTGACTTCTTGCATGCAAGGGACCAT
TGCTTTGCCCACAAACTCCTTAACAACTTGAAA

Alignment

ORF - retro_ptro_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGLEDEQKMLTESGDPEEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDKRV-SSRSHTEEDCT-
          MGLEDEQKML..S.DP.EEEEEEEE.V.PLTTVR.QCEQLEKCVKA...LELCDK.V.SSRSHTEEDC..
Retrocopy MGLEDEQKMLSRS*DPKEEEEEEEE*VNPLTTVR*QCEQLEKCVKAWKQLELCDKCV>SSRSHTEEDCK<

Parental  EELFDFLHARDHCVAHKLFNNLK
          EELFDFLHARDHC.AHKL.NNLK
Retrocopy EELFDFLHARDHCFAHKLLNNLK

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	119.33 RPM
SRP007412_cerebellum	0.00 RPM	133.54 RPM
SRP007412_heart	0.00 RPM	312.53 RPM
SRP007412_kidney	0.00 RPM	151.50 RPM
SRP007412_liver	0.00 RPM	59.22 RPM
SRP007412_testis	0.00 RPM	37.52 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_422 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_422 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_564
Pongo abelii	retro_pabe_516
Callithrix jacchus	retro_cjac_962

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009603	3 retrocopies	retro_btau_1247, retro_btau_691, retro_btau_732,
Callithrix jacchus	ENSCJAG00000021126	5 retrocopies	retro_cjac_1303, retro_cjac_1337, retro_cjac_2726, retro_cjac_3338, retro_cjac_962,
Homo sapiens	ENSG00000173660	5 retrocopies	retro_hsap_2085, retro_hsap_2659, retro_hsap_3200, retro_hsap_348, retro_hsap_564,
Gorilla gorilla	ENSGGOG00000010631	1 retrocopy	retro_ggor_1855,
Macropus eugenii	ENSMEUG00000006850	1 retrocopy	retro_meug_1932,
Mus musculus	ENSMUSG00000063882	4 retrocopies	retro_mmus_1426, retro_mmus_1965, retro_mmus_2126, retro_mmus_894,
Nomascus leucogenys	ENSNLEG00000016523	4 retrocopies	retro_nleu_1152, retro_nleu_1529, retro_nleu_2134, retro_nleu_2212,
Oryctolagus cuniculus	ENSOCUG00000007600	1 retrocopy	retro_ocun_1410,
Otolemur garnettii	ENSOGAG00000001134	2 retrocopies	retro_ogar_487, retro_ogar_763,
Ochotona princeps	ENSOPRG00000016059	1 retrocopy	retro_opri_489,
Pongo abelii	ENSPPYG00000025831	4 retrocopies	retro_pabe_2314, retro_pabe_2653, retro_pabe_516, retro_pabe_7,
Pan troglodytes	ENSPTRG00000000691	4 retrocopies	retro_ptro_1534, retro_ptro_1792, retro_ptro_2246, retro_ptro_422 ,
Rattus norvegicus	ENSRNOG00000012550	1 retrocopy	retro_rnor_1227,
Sorex araneus	ENSSARG00000006763	1 retrocopy	retro_sara_110,
Tupaia belangeri	ENSTBEG00000011608	2 retrocopies	retro_tbel_1692, retro_tbel_2458,
Tarsius syrichta	ENSTSYG00000006572	2 retrocopies	retro_tsyr_1821, retro_tsyr_2156,
Tursiops truncatus	ENSTTRG00000006326	1 retrocopy	retro_ttru_622,