RetrogeneDB ID: retro_opri_347

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_553:193992..194216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000004130
• Aliases: None
• Description: None

Sequence

>retro_opri_347
ATGAAGCTGCCTGCTCATAACCTGCTGAGCTTACATGTGTGAGACGTGGGGCTCTGCAGCTCTCTCCTGTGCCTGCAGGC
CATGGAAGTCCACATCAACTCCGTGGGCTTCAACTCCAACCTCAGTGTGTGAATGGTCCCTGAAGTGGTGTGGTGGTGCT
CTGGGAGACAGCCAACACCCTGCACCTGCCAGAGGTGCCCCAGGAGCCATTCCAGGGCTACGAA

Alignment

ORF - retro_opri_347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.32 %
• Parental protein coverage: 66.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLLTHNLLSSHVRGVGPRGFPLRLQATEVRINPVDFNPDFVARMIPKVEW-AALREAAQTLHLVDLPEQ
          MKL..HNLLS.HV..VG.....L.LQA.EV.IN.V.FN......M.P.V.W...L.E.A.TLHL...P..
Retrocopy MKLPAHNLLSLHV*DVGLCSSLLCLQAMEVHINSVGFNSNLSV*MVPEVVW<VVLWETANTLHLPEVPQE

Parental  PAEGYE
          P..GYE
Retrocopy PFQGYE

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_347 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 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017965	3 retrocopies	retro_amel_125, retro_amel_1748, retro_amel_295,
Bos taurus	ENSBTAG00000008646	1 retrocopy	retro_btau_410,
Callithrix jacchus	ENSCJAG00000018026	1 retrocopy	retro_cjac_2995,
Dasypus novemcinctus	ENSDNOG00000004644	1 retrocopy	retro_dnov_2166,
Equus caballus	ENSECAG00000016960	1 retrocopy	retro_ecab_103,
Echinops telfairi	ENSETEG00000000263	4 retrocopies	retro_etel_256, retro_etel_606, retro_etel_772, retro_etel_986,
Homo sapiens	ENSG00000173113	4 retrocopies	retro_hsap_1853, retro_hsap_2847, retro_hsap_2974, retro_hsap_86,
Gorilla gorilla	ENSGGOG00000001334	3 retrocopies	retro_ggor_1669, retro_ggor_2157, retro_ggor_2867,
Macaca mulatta	ENSMMUG00000019647	2 retrocopies	retro_mmul_1267, retro_mmul_2181,
Ochotona princeps	ENSOPRG00000004130	2 retrocopies	retro_opri_347 , retro_opri_560,
Ictidomys tridecemlineatus	ENSSTOG00000019857	1 retrocopy	retro_itri_208,