RetrogeneDB ID: retro_opri_959

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_50112:1222..1499(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000006462
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000002571
• Aliases: None
• Description: None

Sequence

>retro_opri_959
ATGGCACCCAAGGGCAAATTGGGCATGAGTGGGAAGAAGCAGATACATTTAAGGAATAGAGAGACCTTGGCGTGTACCAG
CCTGTCATTTTGGGGGCCAACTCTGTTTGCTGTCTTGTGACCTTGGTCTTCTTTTCTGTCTCATTTTGGGCCTGGAGGGC
CCTGGGCTGCAGTCTGTCAGTGTCCCGGGCCAGCCAGCACTCTGTGATCTCACAAGGACCAGTGACCTTCTCTGAGTATG
TGTCCTTGGTGGGTGGCGGTGTGGACCTCTGCATGGT

Alignment

ORF - retro_opri_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.73 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPKGKVG-TRKKQIFEENRETLK-FYLRIILGANAIYCLVTLVFFYSSASFWAWMALAFSLAVYGASYH
          MAPKGK.G...KKQI...NRETL...Y...ILGAN...CLVTLVFF..S.SFWAW.AL..SL.V..AS.H
Retrocopy MAPKGKLGMSGKKQIHLRNRETLA<VYQPVILGANSVCCLVTLVFF--SVSFWAWRALGCSLSVSRASQH

Parental  SMSSMARAAFSEDGALV-DWH-GPQHG
          S..S.....FSE...LV..W..GP.HG
Retrocopy SVISQGPVTFSEYVSLV<GWRCGPLHG

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_959 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000026215	2 retrocopies	retro_ocun_1721, retro_ocun_1722,
Ochotona princeps	ENSOPRG00000002571	2 retrocopies	retro_opri_944, retro_opri_959 ,
Sus scrofa	ENSSSCG00000002790	1 retrocopy	retro_sscr_273,