RetrogeneDB ID: retro_opri_88

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2154:126125..126424(-)
• Located in intron of: ENSOPRG00000017358

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1
• Ensembl ID: ENSOPRG00000010887
• Aliases: None
• Description: hematological and neurological expressed 1 [Source:HGNC Symbol;Acc:14569]

Sequence

>retro_opri_88
CTTACCACCTCTACCACCTGCAAAGGGTAGATTCTGAAGCAGGAAGAGCTCCCAAGCTTTACAGCCTCCCTCCAGTTGGG
GGATCCAATCTTTCATGAGACTTTGATGAACCAACAGAAGAACCTGTGACAAAGAACAAACTAACCTCCAGCATCTTTGA
GACAGCTAAGAAAAAAATCTCCCTTCCTGTGCCAAGAGCTGTGGCAGGTGCCAAGTCTGGCAGAGAGGATTCTGAGTCAC
CCAGGCTGCAGAGAAGAAACACCTCTGAAGCTAGCTAGAAAGACTTGTTTGATCTGAAA

Alignment

ORF - retro_opri_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.49 %
• Parental protein coverage: 54.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTTTTFKG-VDPNSRNSSRVLR-PPGGGSNFSLGFDEPAEQPVRKNKMASSIFGTPEENPPSWAKSAGA
          .TT.TT.KG.VD............PP.GGSN.S..FDEP.E.PV.KNK..SSIF.T...........A.A
Retrocopy LTTSTTCKG<VDSEAGRAPKLYSLPPVGGSNLS*DFDEPTEEPVTKNKLTSSIFETAKKKISLPVPRAVA

Parental  KSGSGREDAESSGLQRRN-SEASSGDVLDLK
          ...SGRED.ES..LQRRN.SEAS..D..DLK
Retrocopy GAKSGREDSESPRLQRRNTSEAS*KDLFDLK

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_88 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88 ,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,