RetrogeneDB ID: retro_opri_276

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4512:298996..300052(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP3
• Ensembl ID: ENSOPRG00000004107
• Aliases: None
• Description: CDK5 regulatory subunit associated protein 3 [Source:HGNC Symbol;Acc:18673]

Sequence

>retro_opri_276
CTGCGGGAGCGGCTCCATCACTCGTGCAAGCAGTATGGCATCACGGGAGACAATGTGCGGAGGGAACTGCTGGCTCTGGT
GAATGACCTGCCGGGGAAGCTGGCTGAGATCGGGGCAGCGGCTCAGTCACTGGAAGAGGCCATAGAACTGTACCAGACCT
GCGTGGGCTTCGAGTGTGAAAGCCCCACGGAGCAGGTGCTGCCGATGCTGCGCTATGTACAGGAGCGGGGCAACTCCACA
GTGTACGAGTGGAGGACGGGCATGGAGCCCTCTGTAGTGGAGCGGCCACACCGGGAGGAGCCTGCCGAGCCAGTGGAAGA
GGATGCGATCGACTGGGGTGACTTCGGGATGGAGCCAGCTTTGCAGGCCACTGACGCTGGCATCTCTACCGAGGCCGCTG
GCATCGACTGGGGCATCTCCCTGGCATCAGACCCAAAGGACTCTGGGGGTGATGGCATCGACTGGGGAGATGACGTGGCC
ACGTTGCAGATCACAGTGGTGGAAGCAGGAACTGAGGCTCCAGAAGGTGTCGCTCGGGGCCCAGACGCCCTTACACTCCT
TGAATATCCAGAGACCCGAAATCAGTTCATTGATGAGCTCATGGAGCTTGAGATCTTCCTGTGCCAGAGAGCGGTGGAGA
TGAGCGAGGAGGCAGACATGCTGGCCACGAGCCAGTTCCAGTTCCAGGATGGCTCCCGCCATCCTGCAGGGCCAGACCAA
AGAGCAGATGGTTACCATGGTGGCGACACTGCAGGATCTGATAGGTCGGCTCACCGACCTGCGAATGCAGCACCTGTTTA
TGATCCTGGCCTCGCCCAGGTACGTGGACCGAGTGACCGAGTTCCTCCAGCAGAAGCTGAAGCAGTCCCAGCTGCTGGCG
CTCAAGAAGGAGCTGATGGTGCAGCGGCAACAGGAGGCGCTTCAGGAGCAGGCGGCTCTGGAGCCCAAGCTGGACCTGCT
GCTGGAGAAGACCAAGGAGCTCAGGAAGCTGATTGAGGCCGACATCTCCAAGAGGTTCGGCGGCGGGCGCCCCTGAACCT
GATGGGAACCTCGCTG

Alignment

ORF - retro_opri_276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 69.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRERFHHSCKQYGITGDNVRRELLALVNDLPGQLAEIGAAAQSLGEAIDLYQACVGFVCESPTEQVLPML
          LRER.HHSCKQYGITGDNVRRELLALVNDLPG.LAEIGAAAQSL.EAI.LYQ.CVGF.CESPTEQVLPML
Retrocopy LRERLHHSCKQYGITGDNVRRELLALVNDLPGKLAEIGAAAQSLEEAIELYQTCVGFECESPTEQVLPML

Parental  RYVQERGNSTVYEWRTGMEPSVVERTHREKPSEQLGEDAIDWGDFGMEPALQATDSGISTEATGIDWGIS
          RYVQERGNSTVYEWRTGMEPSVVER.HRE.P.E...EDAIDWGDFGMEPALQATD.GISTEA.GIDWGIS
Retrocopy RYVQERGNSTVYEWRTGMEPSVVERPHREEPAEPVEEDAIDWGDFGMEPALQATDAGISTEAAGIDWGIS

Parental  LESDPKDSGGDGIDWGDDVATSQITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFLSQR
          L.SDPKDSGGDGIDWGDDVAT.QITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFL.QR
Retrocopy LASDPKDSGGDGIDWGDDVATLQITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFLCQR

Parental  AVEMSEEADILAMSQ--FQ-LAPAILQGQTKEQMVTMVATLQDLIGRLTNLRMQHLFMILASPRYVDRVT
          AVEMSEEAD.LA.SQ..FQ..APAILQGQTKEQMVTMVATLQDLIGRLT.LRMQHLFMILASPRYVDRVT
Retrocopy AVEMSEEADMLATSQFQFQ>MAPAILQGQTKEQMVTMVATLQDLIGRLTDLRMQHLFMILASPRYVDRVT

Parental  EFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKELQKLIEADISKRY-GGRP-VNLM
          EFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKEL.KLIEADISKR..GGRP..NLM
Retrocopy EFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKELRKLIEADISKRFGGGRP<LNLM

Parental  GTSL
          GTSL
Retrocopy GTSL

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_276 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108465	1 retrocopy	retro_hsap_2466,
Gorilla gorilla	ENSGGOG00000022994	1 retrocopy	retro_ggor_1535,
Nomascus leucogenys	ENSNLEG00000002109	1 retrocopy	retro_nleu_2448,
Ochotona princeps	ENSOPRG00000004107	2 retrocopies	retro_opri_276 , retro_opri_480,
Pongo abelii	ENSPPYG00000008888	1 retrocopy	retro_pabe_1818,
Pan troglodytes	ENSPTRG00000009345	1 retrocopy	retro_ptro_1425,