RetrogeneDB ID: retro_opri_1008

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_56972:7414..7666(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000004226
• Aliases: None
• Description: None

Sequence

>retro_opri_1008
CAGCTGGAGAAAGCCATCGCTGTCGCCGACCAGAGGCAGAAGGTGGACACGGACGGGGTGGAGCCCATGGAGTCGGTCCT
GGAGGACAAATGTCTATACTTGAGATCCGACAATGTAGTAGAAAGCAACTGTGCTGAAGAACTACTACCAAGCTCCAACT
GTGTCCTGGAGGAATATATTGTGACACCCCCTGCACTTCCCCACAATATCCCTTTGCTGAAGCTGGATGAACTAGAGCCC
TTTCCACACAGC

Alignment

ORF - retro_opri_1008 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLEKAIAFADRLREVNTDGVEPMESVLEDRCLYLRSDNVVEGNCAEELLQNSHCVLEEYFVAPPG---NI
          .LEKAIA.AD....V.TDGVEPMESVLED.CLYLRSDNVVE.NCAEELL..S.CVLEEY.V.PP....NI
Retrocopy QLEKAIAVADQRQKVDTDGVEPMESVLEDKCLYLRSDNVVESNCAEELLPSSNCVLEEYIVTPPALPHNI

Parental  PLPKLDEQEPSPHS
          PL.KLDE.EP.PHS
Retrocopy PLLKLDELEPFPHS

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_1008 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585, retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008 ,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746,
Tarsius syrichta	ENSTSYG00000006845	1 retrocopy	retro_tsyr_1219,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,