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


Retrocopy-Parental alignment summary:






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

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:

ParentalLRERFHHSCKQYGITGDNVRRELLALVNDLPGQLAEIGAAAQSLGEAIDLYQACVGFVCESPTEQVLPML
LRER.HHSCKQYGITGDNVRRELLALVNDLPG.LAEIGAAAQSL.EAI.LYQ.CVGF.CESPTEQVLPML
RetrocopyLRERLHHSCKQYGITGDNVRRELLALVNDLPGKLAEIGAAAQSLEEAIELYQTCVGFECESPTEQVLPML
ParentalRYVQERGNSTVYEWRTGMEPSVVERTHREKPSEQLGEDAIDWGDFGMEPALQATDSGISTEATGIDWGIS
RYVQERGNSTVYEWRTGMEPSVVER.HRE.P.E...EDAIDWGDFGMEPALQATD.GISTEA.GIDWGIS
RetrocopyRYVQERGNSTVYEWRTGMEPSVVERPHREEPAEPVEEDAIDWGDFGMEPALQATDAGISTEAAGIDWGIS
ParentalLESDPKDSGGDGIDWGDDVATSQITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFLSQR
L.SDPKDSGGDGIDWGDDVAT.QITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFL.QR
RetrocopyLASDPKDSGGDGIDWGDDVATLQITVVEAGTEAPEGVARGPDALTLLEYPETRNQFIDELMELEIFLCQR
ParentalAVEMSEEADILAMSQ--FQ-LAPAILQGQTKEQMVTMVATLQDLIGRLTNLRMQHLFMILASPRYVDRVT
AVEMSEEAD.LA.SQ..FQ..APAILQGQTKEQMVTMVATLQDLIGRLT.LRMQHLFMILASPRYVDRVT
RetrocopyAVEMSEEADMLATSQFQFQ>MAPAILQGQTKEQMVTMVATLQDLIGRLTDLRMQHLFMILASPRYVDRVT
ParentalEFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKELQKLIEADISKRY-GGRP-VNLM
EFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKEL.KLIEADISKR..GGRP..NLM
RetrocopyEFLQQKLKQSQLLALKKELMVQRQQEALQEQAALEPKLDLLLEKTKELRKLIEADISKRFGGGRP<LNLM
ParentalGTSL
GTSL
RetrocopyGTSL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_276 was not experimentally validated.

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 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001084651 retrocopy
Gorilla gorilla ENSGGOG000000229941 retrocopy
Nomascus leucogenys ENSNLEG000000021091 retrocopy
Ochotona princeps ENSOPRG00000004107 2 retrocopies
retro_opri_276 , retro_opri_480,
Pongo abelii ENSPPYG000000088881 retrocopy
Pan troglodytes ENSPTRG000000093451 retrocopy



Copyright © RetrogeneDB 2014-2017