RetrogeneDB ID:

retro_pcap_152

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_116772:6932..7241(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL31
Ensembl ID:ENSPCAG00000004787
Aliases:None
Description:ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]


Retrocopy-Parental alignment summary:






>retro_pcap_152
ATGGATCCCATAAAAAAGGATGATGAGAAGATGGGCCACTCTGCTTTCAGCAAAGTGGTGACCAGAGCTCACCATCAACA
TTAACAAGCACATCCACGGCACAAGCTTCAAGAAACACCTTAGGCACTGAAAATTATCTGGAAATTTGCTGTGAAGGAGC
TGAGAACATCAAATTGGCACGCAGACACCAGGCTCAACAAAGCTGTCTGGGCCAAAGGAATAAAGAATGTTCTTTACCCT
ATCCATATGAGGCTGTCCAGAAAACATAATGAGGCTGAAAGCTATCTAAACAGGCTCTATATGTTCATT

ORF - retro_pcap_152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.94 %
Parental protein coverage: 84.8 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
M.P.KK..EK..G.SA...VVTR......H...H........P.ALK.I.KFA.KE..T.....DTRLNK
RetrocopyMDPIKKDDEKM-GHSAFSKVVTRAH--HQH*QAHPRHKLQETP*ALKIIWKFAVKELRTSNWHADTRLNK
ParentalAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLV
AVWAKGI.NV.Y.I..RLSRK.NE.E...N.LY...
RetrocopyAVWAKGIKNVLYPIHMRLSRKHNEAESYLNRLYMFI

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_152 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 12 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000157283 retrocopies
Felis catus ENSFCAG0000002643013 retrocopies
Latimeria chalumnae ENSLACG000000136031 retrocopy
Macropus eugenii ENSMEUG000000009638 retrocopies
Myotis lucifugus ENSMLUG0000000250721 retrocopies
Otolemur garnettii ENSOGAG0000001449410 retrocopies
Procavia capensis ENSPCAG00000004787 10 retrocopies
Pongo abelii ENSPPYG000000258704 retrocopies
Rattus norvegicus ENSRNOG000000135088 retrocopies
Sus scrofa ENSSSCG000000081704 retrocopies
Sus scrofa ENSSSCG000000251806 retrocopies
Tursiops truncatus ENSTTRG0000001644724 retrocopies



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