RetrogeneDB ID:

retro_pcap_156

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_11921:42424..42938(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTL
Ensembl ID:ENSPCAG00000013227
Aliases:None
Description:ferritin, light polypeptide [Source:HGNC Symbol;Acc:3999]


Retrocopy-Parental alignment summary:






>retro_pcap_156
ATAAGCTCAAACATCTGTCAGAATTACTCTGCCAAAGCACAGGCTAGTGTTAACCACCTGGTCAACCTGTGTCTGCCAGC
CTCCTGCATCTACTCTCTGAGCTTGTATTTCTACTGAGACCGTGTAGATTTGGAAGGCATGGGATACTTTTTCCACTATC
AGGCAAAGGAGAAGCAGAAACATATGCACTGTCTCTTGAAGGTGCAAACCAGTGTAGTGGCCATGCTATCTTCCAGGACA
CACAGAAGCTGTCCTGAGGTAAGTGGGGTAGAATCCTGGATGCCACAGAAGTTGCCCTGGCCCTGAATAAGAACCTGAAC
CAGGCCCTTGTGGATCTGTACACTATAGGTTCTACCAGCGCAGCCCACGATTTCTGTGACTTTATCAAGAACCATTTCCT
CACTGAGGTAAAACTCTTCAGGATAAGTGGTGATCACGTGACCAGTCTCTGCAGGCATTATTTCCAAACTGAGCTGGATG
AGTAACTCTTCAGAGGCTTACCCTCAAGCATGAC

ORF - retro_pcap_156 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.54 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSSQIRQNYSADAEANVNLLVNLHLRASYTYLSLGFYFDRDDVALQGVGHFFRELAKEKREGAERLLKLQ
.SS.I.QNYSA.A.A.VN.LVNL.L.AS..Y.SL..YF..D.V.L.G.G.FF...AKEK......LLK.Q
RetrocopyISSNICQNYSAKAQASVNHLVNLCLPASCIY-SLSLYFY*DRVDLEGMGYFFHYQAKEKQKHMHCLLKVQ
Parental-NQRGGRALFQDVEKPSRDEWGETLDAMEAALALELSLNEALLKLHAVASAQADPHLCDFLENHFLDEEV
.NQ..G.A.FQD..K.S...WG..LDA.E.ALAL...LN.AL..L....S..A....CDF..NHFL..EV
Retrocopy<NQCSGHAIFQDTQKLS*GKWGRILDATEVALALNKNLNQALVDLYTIGSTSAAHDFCDFIKNHFL-TEV
ParentalKLIKKMGDHLTNIRRVVGSQAGLGEYLF-ERLTLKHD
KL....GDH.T...R....Q..L.E.LF..RLTLKHD
RetrocopyKLFRISGDHVTSLCRHY-FQTELDE*LF<QRLTLKHD

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_156 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 23 parental genes, and 314 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001458227 retrocopies
Bos taurus ENSBTAG0000001334333 retrocopies
Canis familiaris ENSCAFG000000038611 retrocopy
Callithrix jacchus ENSCJAG0000000025013 retrocopies
Cavia porcellus ENSCPOG000000205581 retrocopy
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
Felis catus ENSFCAG0000000334837 retrocopies
Gorilla gorilla ENSGGOG000000119999 retrocopies
Loxodonta africana ENSLAFG0000003124811 retrocopies
Macaca mulatta ENSMMUG000000039099 retrocopies
Mustela putorius furoENSMPUG0000000330429 retrocopies
Mus musculus ENSMUSG000000507081 retrocopy
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
Procavia capensis ENSPCAG0000001037713 retrocopies
Procavia capensis ENSPCAG00000013227 6 retrocopies
Pan troglodytes ENSPTRG0000001126811 retrocopies
Rattus norvegicus ENSRNOG000000208437 retrocopies
Sus scrofa ENSSSCG0000000315333 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000206397 retrocopies



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