RetrogeneDB ID: retro_opri_968

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5125:144161..144498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIF
• Ensembl ID: ENSOPRG00000012184
• Aliases: None
• Description: macrophage migration inhibitory factor (glycosylation-inhibiting factor) [Source:HGNC Symbol;Acc:7097]

Sequence

>retro_opri_968
ATGCCGATGTTCGTCGAGAACACCAACGTGCCCCGCGCCTCCGTGCCAGATGGGCTCCGGTCCGAGCTCACCCAGCAGCT
GGCGCAGGCCACGGGCAAGCCGGTGCAATACATCGAAGTGCACGTGGTCCCGGACCAGCATTCGGAGGCTCCAGCGAGCC
CTGCGCCTCTGCAGTCTGCACAGCATAGGCAAAATAGGCGGTGCACAGAACCACACCTACAGCAAGCTGCTTTGCGGCCT
ACTGGCCGAGCGCCTGCGGGTCAGCCCAGACAGGATCTACATCAACTACTATGACATGAGTGCGGCCAACATGGGCTGGA
ACGGCTCTACCTTCGCC

Alignment

ORF - retro_opri_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMVVNN--VPRASV-DGL-SELTQQLAQVTSKPAQYIAVHVVPDQLMAFSGSSEP-CALCSLHSIGKIG
          MPM.V.N..VPRASV.DGL.SELTQQLAQ.T.KP.QYI.VHVVPDQ......S..P.C.L...HSIGKIG
Retrocopy MPMFVENTNVPRASVPDGLRSELTQQLAQATGKPVQYIEVHVVPDQHSEAPASPAP>CSL---HSIGKIG

Parental  AAQNRTYSKLLCGLLAERLRISPDRIYINYYDMSAANVGWNGSTFA
          .AQN.TYSKLLCGLLAERLR.SPDRIYINYYDMSAAN.GWNGSTFA
Retrocopy GAQNHTYSKLLCGLLAERLRVSPDRIYINYYDMSAANMGWNGSTFA

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_968 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 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010668	3 retrocopies	retro_cjac_2903, retro_cjac_3132, retro_cjac_357,
Cavia porcellus	ENSCPOG00000013520	1 retrocopy	retro_cpor_879,
Dasypus novemcinctus	ENSDNOG00000014555	1 retrocopy	retro_dnov_36,
Equus caballus	ENSECAG00000012792	1 retrocopy	retro_ecab_1122,
Echinops telfairi	ENSETEG00000012052	3 retrocopies	retro_etel_2001, retro_etel_2046, retro_etel_509,
Mus musculus	ENSMUSG00000033307	8 retrocopies	retro_mmus_1573, retro_mmus_1759, retro_mmus_1878, retro_mmus_2182, retro_mmus_2444, retro_mmus_3016, retro_mmus_3315, retro_mmus_489,
Ochotona princeps	ENSOPRG00000012184	1 retrocopy	retro_opri_968 ,
Rattus norvegicus	ENSRNOG00000006589	6 retrocopies	retro_rnor_137, retro_rnor_1608, retro_rnor_1644, retro_rnor_2263, retro_rnor_31, retro_rnor_361,