RetrogeneDB ID: retro_opri_464

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_12731:47966..48472(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000007978
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC34
• Ensembl ID: ENSOPRG00000001017
• Aliases: None
• Description: cell division cycle 34 [Source:HGNC Symbol;Acc:1734]

Sequence

>retro_opri_464
CTTAAGTTCCCCCTCGACTACCCGTATTCCCCACCAGCTTTCCGGTTCCTGACCAAGATGTGGCACCCCAACATCTATGA
GACAGGAGACGTGTGCATCTCCATCCTGCACCCCCCAGCTGACGACCCCCAGAGCGGGGAGCTGCCCTCGGAGCGGTGGA
ACCCCACGCAGAACGTCAGGACCATCCTCCTGAGTGTGATCTCGCTCCTGAAGGAGCCCAATACCTTCTCGCCGGCCAAC
GTGGACGCCTCTGTGATGTACAGGAAGTGGAAGGAGAGCAGAGGGAAGGACCGGGAGTACACAGATATCATCCGGAAGCA
GATCTGGGGACCAAGGTGGACGCAGAGCGCGACGGTGTCAAGGTGCCCACGACACTGGCCGAGTACTGTGTGAAAACCAA
GGCGCCGGTGCCCGAGGAGGGCTCAGACCTCTTCTACGATGACTACTACGAGGACGGCGAGGGGGTCGAGGAGGAGGACT
CGGGCCCCGAGGAGGCCTGAGGCGGC

Alignment

ORF - retro_opri_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 73.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKFPLDYPYSPPAFRFLTKMWH-NIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLL
          LKFPLDYPYSPPAFRFLTKMWH.NIYETGDVCISILHPP.DDPQSGELPSERWNPTQNVRTILLSVISLL
Retrocopy LKFPLDYPYSPPAFRFLTKMWHPNIYETGDVCISILHPPADDPQSGELPSERWNPTQNVRTILLSVISLL

Parental  NEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQV-LGTKVDAERDGVKVPTTLAEYCVKTKAPVPE
          .EPNTFSPANVDASVMYRKWKES.GKDREYTDIIRKQ..LGTKVDAERDGVKVPTTLAEYCVKTKAPVPE
Retrocopy KEPNTFSPANVDASVMYRKWKESRGKDREYTDIIRKQI<LGTKVDAERDGVKVPTTLAEYCVKTKAPVPE

Parental  EGSDLFYDDYYEDGEGEGEADSCFGDEEEDSG
          EGSDLFYDDYYEDGEG..E.DS..G.EE...G
Retrocopy EGSDLFYDDYYEDGEGVEEEDS--GPEEA*GG

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_464 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464 ,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,