RetrogeneDB ID: retro_pabe_516

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:42309573..42309842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRH
• Ensembl ID: ENSPPYG00000025831
• Aliases: None
• Description: ubiquinol-cytochrome c reductase hinge protein [Source:HGNC Symbol;Acc:12590]

Sequence

>retro_pabe_516
GGACTGGAGGATGAGCAAAAGATGCTGAACAGGTCCTGAGATCCTAAGGAGGAGGAAGAGGAAGAGGAGGAATGAGTGAA
TCCCCTAACAACAGTGAGACAGCAATGTGAGCAGTTGGAGAAATGTGTAAAGGCCTGGGAGCAGCTAGAGCTCTGTGACA
AGCGTGTATCCTTTCGATCACATACAGAAGAGGATTGCAAGAGGAGCTCTTTGACTTCTTGCATGCAAGGGACCATTGCT
TTGCCCACAAACTCCTTAACAACTTGAAA

Alignment

ORF - retro_pabe_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLEDEQKMLTESGDPEEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSHTEEDC-TEE
          GLEDEQKML..S.DP.EEEEEEEE.V.PLTTVR.QCEQLEKCVKA.E.LELCD.RVS.RSHTEEDC..EE
Retrocopy GLEDEQKMLNRS*DPKEEEEEEEE*VNPLTTVRQQCEQLEKCVKAWEQLELCDKRVSFRSHTEEDC<QEE

Parental  LFDFLHARDHCVAHKLFNNLK
          LFDFLHARDHC.AHKL.NNLK
Retrocopy LFDFLHARDHCFAHKLLNNLK

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	0.06 RPM	95.93 RPM
SRP007412_cerebellum	0.12 RPM	79.28 RPM
SRP007412_heart	0.12 RPM	135.59 RPM
SRP007412_kidney	0.00 RPM	114.39 RPM
SRP007412_liver	0.00 RPM	37.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_516 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_516 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_564
Pan troglodytes	retro_ptro_422
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,