RetrogeneDB ID: retro_opri_1073

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6601:45510..46266(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000002663
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSOPRG00000010353
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_opri_1073
GCTGTCGGAGGAGCAGGTGTAGAAGGCTGGGAAGATGCTGTGGAGTTTGTTCCCGGGCAGCCCTATCGGGGCCGCGGGGT
GGCTTCCATTCCTGAAGCGCCTCCCCAGGGCTCAGAGGTGGTCGAGAGGGAGCAGGTGGCTGTGGGCAGGGGGGTGCAAC
TTTGCCCTCACGCTGCCAGGGGAGAATGCTTCCGTGGGGAGAGCTGTATGTATCTGCACGGAGAGGTATGCGACATGTGT
GGGCTCCAGGCCTTGCACCCCATGGATGCCGCGCAGAGGGCAGACCATAGGCAGGCCTGCATGGAGGCACATGAGAAAGA
TATGGAGCTGTCATTTGCAGTGCAACGCAGCATGGATAAGGTGTGCGGCATCTGCATGGAGGTGGTGTACGACAAGGCCA
ACCCCAGCGACCGCCGCTTTGGCATCCTGTCCAACTGCAGCCATCCCTACTGCCTCAAGTGTATCCGTAGGTGGCGACGC
GCCAGACACTTTGAGAATAGGATCGTCAAGTCCTGCCCGCAGTGCAGGGTCACCTCCAACTTCGTCATTCCCAGTGAGTT
CTGGGTGGAGGAAGAGGAAGAGAAGGAGAAACTCATTCAGCAGTACAAGGAGGCTCTGAGCAACAAGCCCTGTCGGCATT
TTGCGGAAGGCAGAGGCCACTGCCCCTTTGGAGAGCACTGCTTTTATAAGCACTCGTCCCCTGAGCGCCAGGGAGAGGAG
CCTCCCGGGCAGGGCGGGGGCCCATCCCTCACCTAC

Alignment

ORF - retro_opri_1073 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 52.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATVGAGSEDWVNAIEFVPGQPYCGRTASSCTEAPPQGSVTQEESEKEQTAAETKKQLCPYAAVGECRYGE
          A..GAG.E.W..A.EFVPGQPY.GR...S..EAPPQGS...E..E.EQ.A.....QLCP.AA.GEC..GE
Retrocopy AVGGAGVEGWEDAVEFVPGQPYRGRGVASIPEAPPQGS---EVVEREQVAVGRGVQLCPHAARGECFRGE

Parental  NCVYLHGDSCDMCGLQVLHPTDAAQRSQHIKSCIEAHEKDMELSFAVQRSKDLLCGICMEVVYEKANPSE
          .C.YLHG..CDMCGLQ.LHP.DAAQR..H...C.EAHEKDMELSFAVQRS.D..CGICMEVVY.KANPS.
Retrocopy SCMYLHGEVCDMCGLQALHPMDAAQRADHRQACMEAHEKDMELSFAVQRSMDKVCGICMEVVYDKANPSD

Parental  RRFGILSNCSHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLIQKYKEAMS
          RRFGILSNCSH.YCLKCIR.WR.A..FE..I.KSCP.CR.TSNFVIPSE.WVEE.EEK.KLIQ.YKEA.S
Retrocopy RRFGILSNCSHPYCLKCIRRWRRARHFENRIVKSCPQCRVTSNFVIPSEFWVEEEEEKEKLIQQYKEALS

Parental  NKACRYFDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRY
          NK.CR.F.EGRG.CPFG..CFYKH..P....EEP..Q..G.S..Y
Retrocopy NKPCRHFAEGRGHCPFGEHCFYKHSSPERQGEEPPGQGGGPSLTY

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_1073 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073 ,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,