RetrogeneDB ID: retro_opri_36

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1219:135121..135547(+)
• Located in intron of: ENSOPRG00000012175

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSOPRG00000008117
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_opri_36
ATGTGAATGGATGGTGATAGTTCGGCCACAGATGCTTTGCAGCTGGGCATTTCTGCAGGCTACATTGGAGGGAGCCACTA
CGTCATACAGCCCCATGATGATGCTGAGGACAGCATGAATGATCACAAAGACACAAATGGCTCAAAAGAAAGTTTCTGAG
AACAAGATATCAATCTTCCAATTGCAGATGTGGCTAGGTTAATGAAGAATGCCATACCTCAAACAGGAAAGGTTGCAAAA
GATGCCAAAGAATGTGTTGAAGAGTGTGTGAGTGAGTTTATTAGCTTTATAACATCTGAAGCAAGTGAGAGGTGCCATCA
GGAGAAACGGAAGACAATCAACGGGGAGGACATTCTCTTTGCCATGTCCACCCTGGGCTTTGACAGTTACGTGGAGCCTC
TGAAGCTGTGCCTGCAGAAATCCAGG

Alignment

ORF - retro_opri_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKN
          M.MDGDSS.TDA.QLGISA.YIGGSHYVIQPHDD.EDSMNDH.DTNGSKESF.EQDI.LPIA.VAR.MKN
Retrocopy M*MDGDSSATDALQLGISAGYIGGSHYVIQPHDDAEDSMNDHKDTNGSKESF*EQDINLPIADVARLMKN

Parental  AIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQK
          AIPQTGK.AKDAKECV.ECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKL.LQK
Retrocopy AIPQTGKVAKDAKECVEECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLCLQK

Parental  FR
          .R
Retrocopy SR

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_36 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Dasypus novemcinctus	ENSDNOG00000009984	3 retrocopies	retro_dnov_1536, retro_dnov_758, retro_dnov_855,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36 , retro_opri_657,
Pongo abelii	ENSPPYG00000004892	3 retrocopies	retro_pabe_2201, retro_pabe_2803, retro_pabe_3319,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,