RetrogeneDB ID:

retro_pcap_457

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:scaffold_97327:1606..1889(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SCOC
Ensembl ID:ENSPCAG00000003165
Aliases:None
Description:short coiled-coil protein [Source:HGNC Symbol;Acc:20335]


Retrocopy-Parental alignment summary:






>retro_pcap_457
AAACCTCAGGCGTTTTCCCAACCCTTCTACCTCCTGGTGCCTCAAAGGGCAGATCACTCATCAAGAATTTTGTAGCCAAC
ACCCAAAAGCTTGTTACCTGAGATGACGGATGTTGACATGGATGCAGTTGATGCTGAAAATCAGGTGGAACTGGAGGAAA
AAAACCCGACTTCTTAATCAAGTGTTAGAACTTCAACACACTCTTGAAGCTCTCACTGCAAGAGCTGGTGCAGTTAAGAC
AGAAAATGTGAAGCTAACATCAGAAATCCAAGCTCTAGGACAA

ORF - retro_pcap_457 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.89 %
Parental protein coverage: 59.49 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQPGLSSESLLLPAPLTAEYSLRILYPRPQRWSPKMMNADMDAVDAENQVELEEK-TRLINQVLELQHTLE
.P...S....L..P..A..S.RIL.P.P....P.M...DMDAVDAENQVELEEK.TRL.NQVLELQHTLE
RetrocopyKPQAFSQPFYLLVPQRADHSSRIL*PTPKSLLPEMTDVDMDAVDAENQVELEEK>TRLLNQVLELQHTLE
ParentalDFFVRVVEVKEKHLKLGSENQALGQ
....R...VK....KL.SE.QALGQ
RetrocopyALTARAGAVKTENVKLTSEIQALGQ

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_457 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 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000109572 retrocopies
Bos taurus ENSBTAG000000221092 retrocopies
Canis familiaris ENSCAFG000000036992 retrocopies
Choloepus hoffmanni ENSCHOG0000000060410 retrocopies
Callithrix jacchus ENSCJAG000000030602 retrocopies
Dipodomys ordii ENSDORG000000001778 retrocopies
Erinaceus europaeus ENSEEUG000000111071 retrocopy
Homo sapiens ENSG000001531302 retrocopies
Gorilla gorilla ENSGGOG000000281862 retrocopies
Macropus eugenii ENSMEUG000000145342 retrocopies
Macaca mulatta ENSMMUG000000223511 retrocopy
Monodelphis domestica ENSMODG000000255282 retrocopies
Mustela putorius furoENSMPUG000000161192 retrocopies
Nomascus leucogenys ENSNLEG000000050812 retrocopies
Oryctolagus cuniculus ENSOCUG000000065913 retrocopies
Otolemur garnettii ENSOGAG000000264142 retrocopies
Procavia capensis ENSPCAG00000003165 2 retrocopies
retro_pcap_119, retro_pcap_457 ,
Pongo abelii ENSPPYG000000150772 retrocopies
Pan troglodytes ENSPTRG000000164602 retrocopies
Sarcophilus harrisii ENSSHAG000000034741 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000285293 retrocopies
Tarsius syrichta ENSTSYG000000118146 retrocopies
Tursiops truncatus ENSTTRG000000106771 retrocopy



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