RetrogeneDB ID:

retro_chof_1291

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_25233:5578..6007(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COX5A
Ensembl ID:ENSCHOG00000006108
Aliases:None
Description:cytochrome c oxidase subunit Va [Source:HGNC Symbol;Acc:2267]


Retrocopy-Parental alignment summary:






>retro_chof_1291
TGCTCACACCTGGCTTCTCTTCAGGCTGCCCAGGGTGGCCCTTGAGCCTTCTGCACCTGCCGGGCCCACAGCCCTGCCAC
CATGGTCCAGTCAGTTTGCTGCTACTCCCATGGGTCACCTAAGACAGATGAGGAGTTTGATGCTCGCTGGGTGACATCCT
TCCACAAGCCAGATATCGATGCCTGGGAATTGCATAAAGGGATGAACATGCTTGTTGGCTATGACTTGTTCCTGAACCCA
AAATCATTGGTACTGCTTTGTGGGCATGCTGACGGTTAAACAATTTTGCTAGTACAGTGCGCATCCCTAGAGGTTGTTAA
GGGCAAAGGACCTCATAAGGAAATCTACCCCTATGTCATCTGGAAACTTGGACTAACTTTAAATGAATTGGGAATCTCCA
CTCCAGAGGAACTGAGCCTTGACAAAGTG

ORF - retro_chof_1291 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.18 %
Parental protein coverage: 94.74 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalCAAAAAAAARAGPRGLLHRAPAHGLTAAVQSVRCYSHGSHETDEKFDARWVTYFNKPDIDAWELRKGMNT
C...A...A..G.........AH.....VQSV.CYSHGS..TDE.FDARWVT.F.KPDIDAWEL.KGMN.
RetrocopyCSHLASLQAAQGGP*AFCTCRAHSPATMVQSVCCYSHGSPKTDEEFDARWVTSFHKPDIDAWELHKGMNM
ParentalLVGYD-LVPEPKIIDAALRACRRLNDFASAVRI-LEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEE
LVGYD.LVPEPKII..AL.AC.RLN.FAS.VRI.LEVVK.K.GPHKEIYPYVI..L..TLNELGISTPEE
RetrocopyLVGYD<LVPEPKIIGTALWAC*RLNNFASTVRI>LEVVKGK-GPHKEIYPYVIWKLGLTLNELGISTPEE
ParentalLGLDKV
L.LDKV
RetrocopyLSLDKV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1291 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni 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 24 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086432 retrocopies
Bos taurus ENSBTAG000000172671 retrocopy
Canis familiaris ENSCAFG000000179771 retrocopy
Choloepus hoffmanni ENSCHOG00000006108 4 retrocopies
Callithrix jacchus ENSCJAG000000156136 retrocopies
Cavia porcellus ENSCPOG000000248323 retrocopies
Felis catus ENSFCAG000000105873 retrocopies
Homo sapiens ENSG000001787413 retrocopies
Gorilla gorilla ENSGGOG000000244263 retrocopies
Loxodonta africana ENSLAFG000000062661 retrocopy
Macropus eugenii ENSMEUG000000139422 retrocopies
Myotis lucifugus ENSMLUG000000137021 retrocopy
Macaca mulatta ENSMMUG000000116772 retrocopies
Monodelphis domestica ENSMODG000000281681 retrocopy
Mustela putorius furoENSMPUG000000173141 retrocopy
Mus musculus ENSMUSG000000000882 retrocopies
Nomascus leucogenys ENSNLEG000000147084 retrocopies
Otolemur garnettii ENSOGAG000000056115 retrocopies
Pongo abelii ENSPPYG000000066521 retrocopy
Pan troglodytes ENSPTRG000000072893 retrocopies
Pteropus vampyrus ENSPVAG000000129571 retrocopy
Rattus norvegicus ENSRNOG000000188161 retrocopy
Sarcophilus harrisii ENSSHAG000000159412 retrocopies
Tursiops truncatus ENSTTRG000000080042 retrocopies



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