RetrogeneDB ID: retro_opri_1020

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5859:47670..48136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSOPRG00000010091
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]

Sequence

>retro_opri_1020
AGAAAAGAAGTTTCAGGGTGAAGAATTATAGGCTATTCAATGCAGGAAATGTATGATGGGGTGTCAGAAATGGAGGATTA
CAATCACTTTGTGCCTAGGGGGAAAAAATCAGATGTAATATCAAGATCTGGATATTGTAAAACACAATTAGAAATTGGGT
TTCCACCTGTGCTGGAAAGTTATACACCTGTGACCTTGGTGAAACCACATTTGGTGAAGCATCTTGTACTGATGAGAGAC
TTTTTAATCATTTGGAGACTAATTGGCATTTCAGCCCAGGTCTTCCTGGGTACCCAAGAACTTGTACCTTGAATTTTTCA
ATTTCTTTTTAATTTCACTCAATCCTACATTTTCAACTTGCCATGTTGTGTTTCGAAGAAGTTGTAAAGCAAATGGTTGC
TGCCTTTAAAAGAAGAACATGCAGCTATATGGTCCAGAAGCAAATATACCTCGGGAATTAACGCTT

Alignment

ORF - retro_opri_1020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKEYSERRIIGYSMQEMYDVVSGMEDYKHFVPWCKKSDVISRRSGYCKTRLEIGFPPVLERYTSVVTLVK
          RKE.S..RIIGYSMQEMYD.VS.MEDY.HFVP..KKSDVISR.SGYCKT.LEIGFPPVLE.YT.V.TLVK
Retrocopy RKEVSG*RIIGYSMQEMYDGVSEMEDYNHFVPRGKKSDVISR-SGYCKTQLEIGFPPVLESYTPV-TLVK

Parental  PHLVK-ASCTDGRLFNHLETSWRFSPGLPGYPRTCTLDFSISFEFRSLLHSQLATLFFDEVVKQMVAAFE
          PHLVK.ASCTD.RLFNHLET.W.FSPGLPGYPRTCTL.FSISF.F.S.LH.QLA.L.F.EVVKQMVAAF.
Retrocopy PHLVK<ASCTDERLFNHLETNWHFSPGLPGYPRTCTLNFSISF*FHSILHFQLAMLCFEEVVKQMVAAFK

Parental  RRAC-KLYGPETNIPRELML
          RR.C..LYGPE.NIPREL.L
Retrocopy RRTC<QLYGPEANIPRELTL

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_1020 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020 , retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,