RetrogeneDB ID:

retro_pcap_98

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:GeneScaffold_5983:27950..28330(-)
Located in intron of:ENSPCAG00000010026
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOA
Ensembl ID:ENSPCAG00000009699
Aliases:None
Description:ras homolog family member A [Source:HGNC Symbol;Acc:667]


Retrocopy-Parental alignment summary:






>retro_pcap_98
GCTCTGTGGGACACAGCTGGGCAGGAAGATAATGATCATCTGAGTCCCCTCTCCAACCAAGACATCAATGTTACACTGAT
CTATTTCTCTATCAGCAGTCCTGGAGGTTTATAAAACAATCCCAGGAAAAACAGATTTTGGAAGTTAAGTCTTTCTGTCC
CAATGTGCCCATCACCCTGGCTGAGAACAAGAAAGATCTTCAGAATGATGAGCACATAAGGCAGAAGCTAGCCAAGTTGA
AGCAGGAGCTGGTAAAACCTGATAAAGGGCAGAGAGACTCCAAACAAGACTGGTGCTTTGGGGTAATGGAGTGGCCCACA
AAGATCAAAGATCGAGTGACAGAGGTTTTTGAAAGGGCCGCAAAAGTATCTCTGCAAGCC

ORF - retro_pcap_98 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.38 %
Parental protein coverage: 65.28 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLEN-IP-EKWTPEVKHFCPNVPIILVGNKKDLRN
ALWDTAGQED.D.L.PLS..D..V.L..FSI.SP..L.N.IP.EK...EVK.FCPNVPI.L..NKKDL.N
RetrocopyALWDTAGQEDNDHLSPLSNQDINVTLIYFSISSPGGL*N>IP>EKQILEVKSFCPNVPITLAENKKDLQN
ParentalDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA
DEH.R..LAK.KQE.VKP..G.........FG.ME...K.KD.V.EVFE.A....LQA
RetrocopyDEHIRQKLAKLKQELVKPDKGQRDSKQDWCFGVMEWPTKIKDRVTEVFERAAKVSLQA

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_98 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 36 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082971 retrocopy
Ailuropoda melanoleuca ENSAMEG000000125843 retrocopies
Anas platyrhynchos ENSAPLG000000146871 retrocopy
Bos taurus ENSBTAG000000042792 retrocopies
Canis familiaris ENSCAFG000000230662 retrocopies
Callithrix jacchus ENSCJAG000000039043 retrocopies
Dasypus novemcinctus ENSDNOG000000128256 retrocopies
Dipodomys ordii ENSDORG000000033823 retrocopies
Felis catus ENSFCAG000000274561 retrocopy
Gasterosteus aculeatus ENSGACG000000056701 retrocopy
Gallus gallus ENSGALG000000038061 retrocopy
Gorilla gorilla ENSGGOG000000128431 retrocopy
Gadus morhua ENSGMOG000000081881 retrocopy
Latimeria chalumnae ENSLACG000000169411 retrocopy
Loxodonta africana ENSLAFG000000097268 retrocopies
Meleagris gallopavo ENSMGAG000000022801 retrocopy
Myotis lucifugus ENSMLUG000000139116 retrocopies
Macaca mulatta ENSMMUG000000129621 retrocopy
Monodelphis domestica ENSMODG000000129812 retrocopies
Mus musculus ENSMUSG000000078159 retrocopies
Nomascus leucogenys ENSNLEG000000068394 retrocopies
Ornithorhynchus anatinus ENSOANG000000138071 retrocopy
Oryctolagus cuniculus ENSOCUG000000133233 retrocopies
Otolemur garnettii ENSOGAG000000284891 retrocopy
Oreochromis niloticus ENSONIG000000188841 retrocopy
Procavia capensis ENSPCAG00000009699 3 retrocopies
retro_pcap_191, retro_pcap_202, retro_pcap_98 ,
Pelodiscus sinensis ENSPSIG000000153281 retrocopy
Pan troglodytes ENSPTRG000000149223 retrocopies
Pteropus vampyrus ENSPVAG000000087381 retrocopy
Rattus norvegicus ENSRNOG000000505193 retrocopies
Sarcophilus harrisii ENSSHAG000000163082 retrocopies
Sus scrofa ENSSSCG000000220801 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000045612 retrocopies
Takifugu rubripes ENSTRUG000000119441 retrocopy
Tarsius syrichta ENSTSYG000000082203 retrocopies
Vicugna pacos ENSVPAG000000109313 retrocopies



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