RetrogeneDB ID:

retro_pcap_73

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:GeneScaffold_4068:15978..16421(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS14
Ensembl ID:ENSPCAG00000015960
Aliases:None
Description:ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]


Retrocopy-Parental alignment summary:






>retro_pcap_73
ATGCTACCTCACTAGATGAAGGACAAGAACGAAGAGCAGGTCATCAGCTTTGGACCTCAGATGGCTGAAGGAGAGAATGT
ATTTGGTGTGGGCCACATTCTTATATCCTTCAGTGATACTTTTGTCCATGCCACTGATCTCTTTGACAAGAAACCATCTA
CTGTGTGGCTAGTGTGATAAATGTGAAGACTGACTAAGACAAATCCTCACTATCTGCTCCCATGTTGGCTGCCCAGAATG
TGACCCAGAAGTACAGTAGGCTAGGCACCTCTGCCTTACGTGTCAAACCCCATGCCACAGGTACAAATAGGACCAAGACC
CCCAAGCCAGGGGCCCAATCTTCCCTTAGAGCCCTTGCTTGGTCTAGAATGAAGATCAGGCAGATTCAGGATGTCACCTC
CGTCCCCTCCAACAGCACTCACAGAAAGAGGGGTCACTGTGGT

ORF - retro_pcap_73 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.74 %
Parental protein coverage: 98.01 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK-ETICRVTGGMKVKADRDES
M.P...K.K.EEQVIS.GPQ.AEGENVFGV.HI..SF.DTFVH.TDL..K.ETI..V.....VK.D.D.S
RetrocopyMLPH*MKDKNEEQVISFGPQMAEGENVFGVGHILISFSDTFVHATDLFDK<ETIYCVASVINVKTD*DKS
ParentalSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIDDDTPIPSDS
S..A.MLAAQ.V.Q....LG..AL..K..ATG.NRTKTP.PGAQS.LRALA.S.MKI..I.D.T..PS.S
RetrocopySLSAPMLAAQNVTQKYSRLGTSALRVKPHATGTNRTKTPKPGAQSSLRALAWSRMKIRQIQDVTSVPSNS
ParentalTRRKGGRRG
T.RK.G..G
RetrocopyTHRKRGHCG

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_73 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 21 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000046442 retrocopies
Bos taurus ENSBTAG000000085702 retrocopies
Canis familiaris ENSCAFG000000180942 retrocopies
Callithrix jacchus ENSCJAG000000209811 retrocopy
Cavia porcellus ENSCPOG000000244082 retrocopies
Dipodomys ordii ENSDORG000000071462 retrocopies
Gorilla gorilla ENSGGOG000000245938 retrocopies
Latimeria chalumnae ENSLACG000000161641 retrocopy
Loxodonta africana ENSLAFG000000311952 retrocopies
Macropus eugenii ENSMEUG000000149071 retrocopy
Microcebus murinus ENSMICG000000029002 retrocopies
Myotis lucifugus ENSMLUG000000132794 retrocopies
Macaca mulatta ENSMMUG000000028485 retrocopies
Mustela putorius furoENSMPUG000000137761 retrocopy
Nomascus leucogenys ENSNLEG000000103661 retrocopy
Oryctolagus cuniculus ENSOCUG000000115091 retrocopy
Otolemur garnettii ENSOGAG000000007211 retrocopy
Procavia capensis ENSPCAG00000015960 3 retrocopies
retro_pcap_198, retro_pcap_443, retro_pcap_73 ,
Pan troglodytes ENSPTRG000000174188 retrocopies
Rattus norvegicus ENSRNOG0000001877410 retrocopies
Sorex araneus ENSSARG000000142491 retrocopy



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