RetrogeneDB ID: retro_opri_550

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1669:15298..15658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSOPRG00000002460
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_opri_550
AGAAAAATAAAGAAGCAAAAAAGGCTTCAGGGAACCATGGCTGACCTCGTGTGAGGCAGATCGAAGTCAAGACCTGAGTG
GTGAAGCGACTGGTCAAAGAAAAAGTGAGGTATGAGGAAGAAGCAAAATAGCAAGAAGAAAAGATTGAAAAAAGTGAAAG
CTGAAGTTGGTGACAATTATGCCATTAAAAATCAGGCTGAGATCCTGCAGGAGCCACGTGTGATGACCCCTGACTGCCAG
CACAGGCTGGAGGCCACCTACACTGACCTGCAGCAGATGCTGGAAAGTGAAAAAGACTCAGAAGAAGCTGAAGAGTATAA
AGAAGCATGCGTGGTCCTGGACTCGGTGAAGCTGGAAGCC

Alignment

ORF - retro_opri_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 89.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRPAPARRGAGAMAD-PRVRQIKIKTGVVKRLVKEKVMYEKEAKQQEEKIEK-MKAEDGENYAIKKQAEI
          R......R..G.MAD.PRVRQI..KT.VVKRLVKEKV.YE.EAK.QEEKIEK..KAE.G.NYAIK.QAEI
Retrocopy RKIKKQKRLQGTMAD<PRVRQIEVKT*VVKRLVKEKVRYEEEAK*QEEKIEK>VKAEVGDNYAIKNQAEI

Parental  LQESRMMIPDCQRRLEAAYADLQQ--ESEKDLEEAEEYKEARVVLDSVKLEA
          LQE.R.M.PDCQ.RLEA.Y.DLQQ..ESEKD.EEAEEYKEA.VVLDSVKLEA
Retrocopy LQEPRVMTPDCQHRLEATYTDLQQMLESEKDSEEAEEYKEACVVLDSVKLEA

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_550 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Homo sapiens	ENSG00000171530	3 retrocopies	retro_hsap_3065, retro_hsap_346, retro_hsap_4667,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970,
Otolemur garnettii	ENSOGAG00000010198	1 retrocopy	retro_ogar_3193,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550 , retro_opri_727, retro_opri_879, retro_opri_91,
Pongo abelii	ENSPPYG00000015579	2 retrocopies	retro_pabe_2540, retro_pabe_350,
Pan troglodytes	ENSPTRG00000017013	2 retrocopies	retro_ptro_2067, retro_ptro_274,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,
Ictidomys tridecemlineatus	ENSSTOG00000009840	1 retrocopy	retro_itri_246,
Tupaia belangeri	ENSTBEG00000006034	6 retrocopies	retro_tbel_1073, retro_tbel_113, retro_tbel_1286, retro_tbel_2336, retro_tbel_2905, retro_tbel_756,
Tarsius syrichta	ENSTSYG00000000514	1 retrocopy	retro_tsyr_1038,