RetrogeneDB ID: retro_opri_30

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1123:556622..556979(+)
• Located in intron of: ENSOPRG00000012344

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000014505
• Aliases: None
• Description: None

Sequence

>retro_opri_30
TCTAAGCCCATCCCACGTTATGGTTATAAACCCTCCCCACCAAATGGATGTGGCTCTCCATTGTTTGGTGTCCATATCAA
CATTGGCATCCCTTCCCTGACCAAGTGCTGCAACCAACATGACAGGTGCTATGAGACGTGTGGCAAAAGCAAGAACGACT
GTGATGAGGAATTCCAGTACTGCCTCTCCAAAATCTGCCGGGGTGTGCAGAAAACGCTGGGACTAGCTCAGCACGTGCAA
CCGTGTGAAACAGCAGTGGAGCTCCTGTTTGACAGCGTCATCCACCTGGGCTGTAAGCCCTACCTGGACAGCCAGCGGGC
CACATGCATGTGTCGCTACGAAGAGAAATCTGACCTT

Alignment

ORF - retro_opri_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKPIPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRGVQ
          SKPIPRYGYKPSPPNGCGSPLFGVH.NIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRGVQ
Retrocopy SKPIPRYGYKPSPPNGCGSPLFGVHINIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRGVQ

Parental  KTLGLAQHVQACETAVELLFDSVIHLGCKPYLDSQRAACTCRYEEKSDL
          KTLGLAQHVQ.CETAVELLFDSVIHLGCKPYLDSQRA.C.CRYEEKSDL
Retrocopy KTLGLAQHVQPCETAVELLFDSVIHLGCKPYLDSQRATCMCRYEEKSDL

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_30 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 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30 , retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,