RetrogeneDB ID: retro_opri_160

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3025:188606..188831(-)
• Located in intron of: ENSOPRG00000007127

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFG
• Ensembl ID: ENSOPRG00000015157
• Aliases: None
• Description: glia maturation factor, gamma [Source:HGNC Symbol;Acc:4374]

Sequence

>retro_opri_160
TTCATTGTGTATAGTTATAAATATCAGCATGATGATGGAAAAATTTCACATCCTCTGTGCTTTATTTTCTCCTGTCCTGT
TGAATGAAAACCTGAACAACAGATGATGTATGCTGGGAGTAAGAACAAGCTTAGTCCAAACAGCTGAACTCACAAAGATG
TTTGAAATAAAACTACTGAAGACCTAACTGAAGAGTGATTACATGAGAATCTGGGATTTTTCCGC

Alignment

ORF - retro_opri_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVVYSYKYLHADGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNR-LVQTAELTKVFEI-RTTEDLTEAWLR
          F.VYSYKY.H.DG..S.PLCFIFS.PV..KPEQQMMYAGSKN..LVQTAELTK.FEI..TTEDLTE..L.
Retrocopy FIVYSYKYQHDDGKISHPLCFIFSCPVE*KPEQQMMYAGSKNK>LVQTAELTKMFEI<KTTEDLTEE*LH

Parental  EKLAFFR
          E.L.FFR
Retrocopy ENLGFFR

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_160 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006529	2 retrocopies	retro_dnov_1062, retro_dnov_1435,
Echinops telfairi	ENSETEG00000008573	1 retrocopy	retro_etel_1630,
Gorilla gorilla	ENSGGOG00000006957	1 retrocopy	retro_ggor_1960,
Mus musculus	ENSMUSG00000060791	1 retrocopy	retro_mmus_2800,
Ochotona princeps	ENSOPRG00000015157	2 retrocopies	retro_opri_1160, retro_opri_160 ,
Sarcophilus harrisii	ENSSHAG00000008772	1 retrocopy	retro_shar_803,