RetrogeneDB ID: retro_opri_944

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_48473:5937..6157(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_opri_944
ATGGCACCCAAGGACAATTTGGACGTGAGAGGGAAGAAGTAGATATGTTCAGGGAATAGAGAGACCCTGGAGTTTACCAG
CCCGTTCATCAAGGGGCCAACTCTGTTTATTCTCTTGTGACCTTGGTCTTCTTCTCCTTGTCTGCCTCATTTGGGCCTGG
AGGGCCCTGGGCTGCAGTCTGTCAGTGTCCAGGTCCAGCCAGCACTCTGTGATCACTCTG

Alignment

ORF - retro_opri_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.95 %
• Parental protein coverage: 51.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPKGKVGTR-KKQIFEENRETLKF-YLRIILGANAIYCLVTLVFFYSSASF-WAWMALAFSLAVYGASY
          MAPK.....R.KK.I...NRETL.F.Y.....GAN..Y.LVTLVFF..SASF.WAW.AL..SL.V...S.
Retrocopy MAPKDNLDVRGKK*ICSGNRETLEF<YQPVHQGANSVYSLVTLVFFSLSASF<WAWRALGCSLSVSRSSQ

Parental  HSMSSM
          HS....
Retrocopy HSVITL

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_944 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,