RetrogeneDB ID: retro_opri_489

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_13737:10633..10804(-)
• Located in intron of: ENSOPRG00000010040

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRH
• Ensembl ID: ENSOPRG00000016059
• Aliases: None
• Description: ubiquinol-cytochrome c reductase hinge protein [Source:HGNC Symbol;Acc:12590]

Sequence

>retro_opri_489
ATGGGCCTGGAGGACGAGCAAAAAGTGCTGACAGGGGCCGGAGATCCCAAGGAGGAAGGAGAGGAAGAGGAGGAATTAGT
GGGTCCCCTCAGCACAGCGAGAGAGCAGCGCGAGCAGCTGGAGAAATGTGTCAAGGCCCGGGAGCGAGGAGAGCTCTGTG
GGGAGCGTGTC

Alignment

ORF - retro_opri_489 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 62.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLEDERKMLTGAGDPKEEEEEEEELVDPLATVREQCEQLEKCVKARERLELCDERV
          MGLEDE.K.LTGAGDPKEE.EEEEELV.PL.T.REQ.EQLEKCVKARER.ELC.ERV
Retrocopy MGLEDEQKVLTGAGDPKEEGEEEEELVGPLSTAREQREQLEKCVKARERGELCGERV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_489 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,