RetrogeneDB ID:

retro_pcap_441

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_88344:5124..5406(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC3
Ensembl ID:ENSPCAG00000011858
Aliases:None
Description:actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]


Retrocopy-Parental alignment summary:






>retro_pcap_441
TGTGATCCCAAAAGCCAAGGCAAGAAACCAACCTACACACCAAGAATCACAAAGTTTCTCATTCCTCTGGAGCCCAGTTT
TTCTACTTAATGCCATTTAGGCCAGACCCACAAACAAACAGGAGAGTGAAGTGATGAGGGCCATTTATAGCAGCTAAGGC
AAGATACTGGGCCGAGGCTTTGTGAGAAAGTTTTTGACCCTCTGAATGACAAACCTGGGAATTGATGGACTTGCTTTGTG
AAGAGATAGTTCATGAGCAAATATCTTTCAGCATCTGGACAG

ORF - retro_pcap_441 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.75 %
Parental protein coverage: 52.81 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalCNSKSQGEKEMYTLGITNFPIPGEPGFP-LNAIYAKPANKQEDEVMRA-YLQQLRQETGLRLCEKVFDPL
C..KSQG.K..YT..IT.F.IP.EP.F..LNAI.A.P.NKQE.EVMRA..L.QLRQ.TG.RLCEKVFDPL
RetrocopyCDPKSQGKKPTYTPRITKFLIPLEPSFS>LNAI*ARPTNKQESEVMRA<HL*QLRQDTGPRLCEKVFDPL
ParentalNDKPSKWWTCFVKRQFMNKSLSGPGQ
NDKP...WTCFVKR.FM.K.LS..GQ
RetrocopyNDKPGN*WTCFVKR*FMSKYLSASGQ

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_441 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 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000084561 retrocopy
Callithrix jacchus ENSCJAG000000093601 retrocopy
Dasypus novemcinctus ENSDNOG000000049872 retrocopies
Dipodomys ordii ENSDORG000000082121 retrocopy
Erinaceus europaeus ENSEEUG000000115312 retrocopies
Felis catus ENSFCAG000000041322 retrocopies
Loxodonta africana ENSLAFG000000061663 retrocopies
Macaca mulatta ENSMMUG000000064923 retrocopies
Monodelphis domestica ENSMODG000000116281 retrocopy
Nomascus leucogenys ENSNLEG000000028024 retrocopies
Oryctolagus cuniculus ENSOCUG000000119081 retrocopy
Otolemur garnettii ENSOGAG000000134241 retrocopy
Oreochromis niloticus ENSONIG000000037851 retrocopy
Procavia capensis ENSPCAG00000011858 2 retrocopies
retro_pcap_421, retro_pcap_441 ,
Pongo abelii ENSPPYG000000049476 retrocopies
Sarcophilus harrisii ENSSHAG000000148053 retrocopies
Tupaia belangeri ENSTBEG000000112191 retrocopy
Tarsius syrichta ENSTSYG000000029534 retrocopies
Tursiops truncatus ENSTTRG000000150832 retrocopies
Vicugna pacos ENSVPAG000000084041 retrocopy



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