RetrogeneDB ID:

retro_pcap_217

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_17693:28815..29211(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTH1
Ensembl ID:ENSPCAG00000010377
Aliases:None
Description:ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]


Retrocopy-Parental alignment summary:






>retro_pcap_217
ATGATGACCATATCCCCATCTCAGGTACTCCAGAAGTATAATCAGGACTCAAAGGCATTCATTAAAGCAAGATCAACCTG
GAGCTCTATACCACCTACGTCTACCTGTCCCAGTCTTACTGCTTTGACTGTGATAACGTGGCTTTGAAGAATTTTGCCAA
AATATTTTCTTCACCAATCTCATGAGGAAAGGGAACATGCTGAAGAAGTGATGAAGATGCAAAACCAAATAGGTGGCTGA
ATCTTCCTTCAGGAAATCAAGAAAATCACACTGTGATGACTGGAGAGCAGATGGAATGCAATAGAGTGTGTATTACATTT
GAGAAAACGTATGAATCAGTTACTACTGAAACTGTACAAACTGACGACTGACTGGAATAGACCTTATTTGTGTGAT

ORF - retro_pcap_217 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.44 %
Parental protein coverage: 72.53 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMTTTFPSQVRQNYSQDSEAAINRQ-INLELYASYVYLSMSYYFDRDDVALKNFA-KYFLHQSHEEREHAE
M.T..PSQV.Q.Y.QDS.A.I....INLELY..YVYLS.SY.FD.D.VALKNFA.KYFLHQSHEEREHAE
RetrocopyMMTISPSQVLQKYNQDSKAFIKAR<INLELYTTYVYLSQSYCFDCDNVALKNFA>KYFLHQSHEEREHAE
ParentalKLMKLQNQRGGRIFLNDIK-KPDRDDW-ESGLNAMECALFLEKNVNQSLLDLHKLATEKNDPHLCD
..MK.QNQ.GG.IFL..IK.K...DDW.ES..NA.EC.L.L.K..NQ.LL.L.KL.T..N.P.LCD
RetrocopyEVMKMQNQIGG*IFLQEIK>KSHCDDW<ESRWNAIECVLHLRKRMNQLLLKLYKLTTDWNRPYLCD

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_217 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 257 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000168311 retrocopy
Canis familiaris ENSCAFG000000159011 retrocopy
Callithrix jacchus ENSCJAG0000001908916 retrocopies
Cavia porcellus ENSCPOG000000265863 retrocopies
Dasypus novemcinctus ENSDNOG0000001712883 retrocopies
Felis catus ENSFCAG000000073821 retrocopy
Homo sapiens ENSG0000016799620 retrocopies
Gorilla gorilla ENSGGOG000000277227 retrocopies
Latimeria chalumnae ENSLACG000000174261 retrocopy
Loxodonta africana ENSLAFG0000000482412 retrocopies
Myotis lucifugus ENSMLUG0000002572616 retrocopies
Monodelphis domestica ENSMODG000000075829 retrocopies
Mus musculus ENSMUSG000000246614 retrocopies
Nomascus leucogenys ENSNLEG0000000332129 retrocopies
Oryctolagus cuniculus ENSOCUG000000141084 retrocopies
Procavia capensis ENSPCAG00000010377 13 retrocopies
Procavia capensis ENSPCAG000000132276 retrocopies
Pongo abelii ENSPPYG0000000317312 retrocopies
Rattus norvegicus ENSRNOG000000226199 retrocopies
Sus scrofa ENSSSCG000000145409 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000145211 retrocopy



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