RetrogeneDB ID:

retro_chof_2352

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_67580:3269..3743(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VPS26A
Ensembl ID:ENSCHOG00000007324
Aliases:None
Description:vacuolar protein sorting 26 homolog A (S. pombe) [Source:HGNC Symbol;Acc:12711]


Retrocopy-Parental alignment summary:






>retro_chof_2352
GGCACTGAAGATTGTCTACACACAGAATTTGAATACAATGAATCAAAGTATCATTTAAAGGATGTGACTGTTGGAAAAAT
TTACTTCTTATTAGTAAGAATAAAAATGCAACACATGGAGTTATAACAGATCAAAAAAGAGACCACAGGAATTGGACCCA
GTACCACAAAAGAAACAGAAACAATTGCCAAATGGGAAGTAATGGAGGGGGCACAAGTAAAAGGCGAATCAATCCAATAA
GACTATTTGTAGCGAGGTATGCCCCAACCCCAACAAGGAGAGATGTGAACAAAAACTTTCAGTAAGGTGCTTTTTGAATC
TAGTCCTTGCTGTTGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAGATCATTTGTGGCAGAAAAGCACCTGAAAAACTG
AGGATACCGAGACAAACTTTCACCAGTGAACTGAATCTCTGGAATCACAGGCATCTGCTGAACAGCCTGAAATG

ORF - retro_chof_2352 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.01 %
Parental protein coverage: 55.59 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGIQDCLHIQFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDG
G..DCLH..FEYN.SKYHLKDV.VGKIYFLLVRIK.QHMEL..IKKE.TGIGPSTT.ETETIAK.E.M.G
RetrocopyGTEDCLHTEFEYNESKYHLKDVTVGKIYFLLVRIKMQHMEL*QIKKETTGIGPSTTKETETIAKWEVMEG
ParentalAPVKGESI-PIRLFLAGYDPTPTMRDVNKKF-SVRYFLNLVLVDEEDRRYFKQQEIILWRKAPEKLRKQR
A.VKGESI.PIRLF.A.Y.PTPT.RDVNK.F.SVR.FLNLVL..EEDRRYFKQQEII..RKAPEKLR..R
RetrocopyAQVKGESI<PIRLFVARYAPTPTRRDVNKNF<SVRCFLNLVLAVEEDRRYFKQQEIICGRKAPEKLRIPR
Parental-INFHQRFESPESQASAEQPEM
..NFHQ..ES.ESQASAEQPEM
Retrocopy<TNFHQ*TESLESQASAEQPEM

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_2352 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 13 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000138271 retrocopy
Choloepus hoffmanni ENSCHOG00000007324 5 retrocopies
Callithrix jacchus ENSCJAG000000129071 retrocopy
Equus caballus ENSECAG000000095071 retrocopy
Homo sapiens ENSG000001229581 retrocopy
Gorilla gorilla ENSGGOG000000104331 retrocopy
Microcebus murinus ENSMICG000000149401 retrocopy
Mustela putorius furoENSMPUG000000045191 retrocopy
Nomascus leucogenys ENSNLEG000000115481 retrocopy
Pongo abelii ENSPPYG000000023861 retrocopy
Pan troglodytes ENSPTRG000000025673 retrocopies
Tupaia belangeri ENSTBEG000000153481 retrocopy
Vicugna pacos ENSVPAG000000006301 retrocopy



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