RetrogeneDB ID:

retro_pcap_323

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_36557:17608..18089(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBXN2A
Ensembl ID:ENSPCAG00000011502
Aliases:None
Description:UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]


Retrocopy-Parental alignment summary:






>retro_pcap_323
CTATCATTATAATTACAGGGGGGTTTTAGTAAAGAGGAGGTGGATGTTAAAGTTGAAGATAAGAAAAATGAAGTTTGTGT
GTCAACAAAACCTGTATTCCAGCCCTTCTCATGACAGGGGTCACAGACTAGAAAGTGCATACCAAAAATTGTTCCTAAAG
CAAAGAGTATTGAAGTTGAGAATGAAAACCATCCATGTACTATCCCATTAAACAACTTGGAACCCATCACTAACATACAG
ATCTGTCTAGCCAATGGGAAAAGGATTGTCCAGAAATTTAACATTTCTCATATCGTTAAACCACATCAAAGACTTCATTG
AAAAATACCAAGGATCTCAGAGCAGCTCTCCATTTTCTCTGGCAACAGCTCTTCCTTTCCTCATATTGCTGGATGAGACA
TTCACTGCAGGAGAAGCCAATTTACAGAATGCTATAATCATTCAGAAACTCCAGAGAGCATCTGAGCCCTTCAGAAGACT
T

ORF - retro_pcap_323 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.64 %
Parental protein coverage: 65.04 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLPLELQGAFNKEEVDVKVEDKKNEVCVSTKPVFQPFSGQGHRLGSATPKIVSKLKSTEVENENHPCTIPL
L.L.LQG.F.KEEVDVKVEDKKNEVCVSTKPVFQPFS.QG.......PKIV.K.KS.EVENENHPCTIPL
RetrocopyLSL*LQGGFSKEEVDVKVEDKKNEVCVSTKPVFQPFS*QGSQTRKCIPKIVPKAKSIEVENENHPCTIPL
ParentalNNLEPITNIQIWLANGKRIVQKFNISHRV-SHIKDFIEKSQGSRRGPPFCLATALPFVRLLDETLTLAEA
NNLEPITNIQI.LANGKRIVQKFNISH.V..HIKDFIEK.QGS....PF.LATALPF..LLDET.T..EA
RetrocopyNNLEPITNIQICLANGKRIVQKFNISHIV>NHIKDFIEKYQGSQSSSPFSLATALPFLILLDETFTAGEA
ParentalGLQNAVIIQRLQRAAEPFKGL
.LQNA.IIQ.LQRA.EPF..L
RetrocopyNLQNAIIIQKLQRASEPFRRL

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






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_323 was not experimentally validated.

Retrocopy orthology:
Procavia capensis 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 18 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000016405 retrocopies
Callithrix jacchus ENSCJAG000000076651 retrocopy
Equus caballus ENSECAG000000201441 retrocopy
Echinops telfairi ENSETEG000000026231 retrocopy
Homo sapiens ENSG000001739601 retrocopy
Gorilla gorilla ENSGGOG000000024451 retrocopy
Myotis lucifugus ENSMLUG000000156401 retrocopy
Macaca mulatta ENSMMUG000000064871 retrocopy
Mus musculus ENSMUSG000000206341 retrocopy
Nomascus leucogenys ENSNLEG000000007511 retrocopy
Oryctolagus cuniculus ENSOCUG000000087831 retrocopy
Otolemur garnettii ENSOGAG000000000251 retrocopy
Procavia capensis ENSPCAG00000011502 4 retrocopies
Pan troglodytes ENSPTRG000000117051 retrocopy
Rattus norvegicus ENSRNOG000000049502 retrocopies
Sorex araneus ENSSARG000000101081 retrocopy
Sus scrofa ENSSSCG000000262831 retrocopy
Tupaia belangeri ENSTBEG000000121581 retrocopy



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