RetrogeneDB ID: retro_opri_630

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2035:13257..13470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDRG1
• Ensembl ID: ENSOPRG00000006403
• Aliases: None
• Description: p53 and DNA-damage regulated 1 [Source:HGNC Symbol;Acc:16119]

Sequence

>retro_opri_630
GGGAGCATATTTATCAGGATGGTGCACCCTCCGACCAAGGAAGTGATAAAGAAAGATCAGGATATTTGGAAACAGAAAGG
ACAAACTGCAGAACGAATTAAAGTGGAAATCAACCTCCTCTTTGAGGCCCAAGACAAGCCAGAGCTGAAGGACTTTAACC
TGAACTCCCTCAACCAGGATGAGCTTAAAGCTCTCAATATCATCTTGAAAGGA

Alignment

ORF - retro_opri_630 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSMFIKMPHPQTKEMIEKDQDHLDKEIDRLRKQLKVKVSRLLEAQGKPELKGFNLNPLNQDELKALKVIL
          GS.FI.M.HP.TKE.I.KDQD...K.........KV....L.EAQ.KPELK.FNLN.LNQDELKAL..IL
Retrocopy GSIFIRMVHPPTKEVIKKDQD-IWKQKGQTAERIKVEINLLFEAQDKPELKDFNLNSLNQDELKALNIIL

Parental  KG
          KG
Retrocopy KG

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_630 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020766	1 retrocopy	retro_cjac_3320,
Homo sapiens	ENSG00000088356	1 retrocopy	retro_hsap_1037,
Gorilla gorilla	ENSGGOG00000024924	1 retrocopy	retro_ggor_818,
Macropus eugenii	ENSMEUG00000003915	1 retrocopy	retro_meug_1967,
Myotis lucifugus	ENSMLUG00000007377	1 retrocopy	retro_mluc_348,
Macaca mulatta	ENSMMUG00000000973	1 retrocopy	retro_mmul_824,
Nomascus leucogenys	ENSNLEG00000009712	1 retrocopy	retro_nleu_910,
Oryctolagus cuniculus	ENSOCUG00000016709	1 retrocopy	retro_ocun_1047,
Ochotona princeps	ENSOPRG00000006403	1 retrocopy	retro_opri_630 ,
Pongo abelii	ENSPPYG00000010897	1 retrocopy	retro_pabe_869,
Pan troglodytes	ENSPTRG00000013368	1 retrocopy	retro_ptro_707,