RetrogeneDB ID: retro_opri_410

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_111839:3910..4230(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBX1
• Ensembl ID: ENSOPRG00000006728
• Aliases: None
• Description: ring-box 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:9928]

Sequence

>retro_opri_410
ATGGTACCAGTGATGGATATGGATACCCAGAGCAGCGCTGATAGCGGCCTGGGGAAGAAGCACTTTGACACGAAAAGGTG
GAATGCGCTAGCCCTCTGGGCCTGGGGTGTTGTGGTGGACAACTGTACCCCCTGCAGGAAACACATCATGGATCTGTGCA
TGGAGTGTCAGGCTAAGCAGGGGTCCGCTGCCTCGGAAGAGCGCACCGTGGCGTGGGCCATCCGTAATCACACTTTCACT
TCCACTGCATCTCTCGCTGACTCGAAACATGGCAGGTGTGTCCCTTGGGCAACCAAGAGTGGAAGTTCCAAAAGTATGGG

Alignment

ORF - retro_opri_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTV
          M...MD.DT.S...SG.GKK.F..K.WNA.ALWAW..VVDNC..CR.HIMDLC.ECQA.Q.SA.SEE.TV
Retrocopy MVPVMDMDTQSSADSGLGKKHFDTKRWNALALWAWGVVVDNCTPCRKHIMDLCMECQAKQGSAASEERTV

Parental  AWGVCNHA-FHFHCISRWLKTRQVCPLDNREWEFQKYG
          AW...NH..FHFHCISR.L.T.QVCPL.N.EW.FQKYG
Retrocopy AWAIRNHT<FHFHCISR*LETWQVCPLGNQEWKFQKYG

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_410 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 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030225	2 retrocopies	retro_btau_1415, retro_btau_61,
Callithrix jacchus	ENSCJAG00000004763	3 retrocopies	retro_cjac_1267, retro_cjac_1955, retro_cjac_1962,
Dasypus novemcinctus	ENSDNOG00000007595	1 retrocopy	retro_dnov_433,
Homo sapiens	ENSG00000100387	1 retrocopy	retro_hsap_2118,
Loxodonta africana	ENSLAFG00000008795	1 retrocopy	retro_lafr_943,
Microcebus murinus	ENSMICG00000008019	1 retrocopy	retro_mmur_750,
Myotis lucifugus	ENSMLUG00000007815	4 retrocopies	retro_mluc_1259, retro_mluc_1712, retro_mluc_20, retro_mluc_244,
Macaca mulatta	ENSMMUG00000012642	3 retrocopies	retro_mmul_702, retro_mmul_974, retro_mmul_996,
Monodelphis domestica	ENSMODG00000013054	1 retrocopy	retro_mdom_626,
Mus musculus	ENSMUSG00000022400	1 retrocopy	retro_mmus_1633,
Nomascus leucogenys	ENSNLEG00000015436	1 retrocopy	retro_nleu_1956,
Ochotona princeps	ENSOPRG00000006728	2 retrocopies	retro_opri_410 , retro_opri_649,
Pongo abelii	ENSPPYG00000011861	2 retrocopies	retro_pabe_1986, retro_pabe_1987,
Pan troglodytes	ENSPTRG00000014417	1 retrocopy	retro_ptro_1550,
Rattus norvegicus	ENSRNOG00000019214	2 retrocopies	retro_rnor_1890, retro_rnor_2724,
Ictidomys tridecemlineatus	ENSSTOG00000015580	1 retrocopy	retro_itri_888,
Tupaia belangeri	ENSTBEG00000009043	4 retrocopies	retro_tbel_1175, retro_tbel_3306, retro_tbel_3756, retro_tbel_3805,
Tursiops truncatus	ENSTTRG00000012018	2 retrocopies	retro_ttru_1419, retro_ttru_583,
Vicugna pacos	ENSVPAG00000004894	2 retrocopies	retro_vpac_207, retro_vpac_502,
Drosophila melanogaster	FBgn0025638	1 retrocopy	retro_dmel_55,