RetrogeneDB ID:

retro_chof_753

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_143080:2775..3599(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VRK2
Ensembl ID:ENSCHOG00000003299
Aliases:None
Description:vaccinia related kinase 2 [Source:HGNC Symbol;Acc:12719]


Retrocopy-Parental alignment summary:






>retro_chof_753
AGTGATGCACCCTGTGTTGTAAAAGCGGAACCCAGTGGCAATGGACTGCTCATTACTGAATTAAAGTTCTACCAGCGAGC
TGCTAAACCAGAGCAAATTCAGAAATGGATTCATTCCCATAAACTGAAGTACCTGGGTGTTCCTAAGTATTGGGGGTCTG
GTCTACATGATAAAAATGGAAAAAGTTATAGGTTTATGATAATGGATCGCTTTGGGAGTGACCGTCAGAAAATATATGAA
GCAAATGCCAAAAGATTTTCTCAAAAGACTGTTTTGAAGCTAAGCTTAAGAATTCTGGATATTCTGGAATATATCCATGA
GCATGAATATGTACACGGAGATATCAAGGCCTCAAATCTTCTTCTGAGCTACAAGAATCCTGACCAGGTGTACCTGGTAG
ATTATGGCCTTGCTGATCGATACTGTCCAGAAAGGAGTCCATAAGGAATACAAAGAAGACCCCAAAAGATGTCATGATGG
CACTCTTGAATTCACCAGCACTGATGCACAATGGCGTGGCTCCCTCAAGACGGGGTGATTTGGAAATACTTGGTTATTGC
ATGATCTGGTGGCTCAGTGGCTGTCTTCCTTGGGAGGATAATTTGAAAGATCCTAACTATGTTAGAGGTTCCAAACTTAG
ATACAGAGAAAATATTGCCGGTTTGGTGGACAAATGTTTTCCTGAGAAAAACAAACCAGATGAAATTGCTAAATACATGG
AAACAGTGAAATTACTGGACTATACCGAAAAACCTCATTATCAAAATTTACGAGATATACTTTTGCAAGGACTCAAAGCT
ATAGGAAGTAAGGATGATGGCACA

ORF - retro_chof_753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.26 %
Parental protein coverage: 53.85 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNDARHVIKVEYQENGPLFSELKFYQRAAKKEYIKRWIALKQLDYLGIPLFYGSGLTTFKGRSYRFMVMER
.DA..V.K.E...NG.L..ELKFYQRAAK.E.I..WI....L.YLG.P...GSGL....G.SYRFM.M.R
RetrocopySDAPCVVKAEPSGNGLLITELKFYQRAAKPEQIQKWIHSHKLKYLGVPKYWGSGLHDKNGKSYRFMIMDR
ParentalLGKDLQKISDQNGT-FKKSTVLHLGIRMLDVLEYIHENEYIHGDIKAANLLLGYKNPEQVYLADYGLSYR
.G.D.QKI...N...F...TVL.L..R.LD.LEYIHE.EY.HGDIKA.NLLL.YKNP.QVYL.DYGL..R
RetrocopyFGSDRQKIYEANAKRFSQKTVLKLSLRILDILEYIHEHEYVHGDIKASNLLLSYKNPDQVYLVDYGLADR
ParentalYCPN-GNHKEYQENPRKGHNGTIETSLD-AHKGVALSRRSDLEILGYCMLRWLCGKLPWERNLKDPVAVQ
YCP..G.HKEY.E.P...H.GT.E......H.GVA.SRR.DLEILGYCM..WL.G.LPWE.NLKDP..V.
RetrocopyYCPE>GVHKEYKEDPKRCHDGTLEFTST>MHNGVAPSRRGDLEILGYCMIWWLSGCLPWEDNLKDPNYVR
ParentalTAKTNLLDELPESVFKWAPSGSSCYEIAQFLACAHSLAYDEKPDYQILKKILNPGGIPLGPLEFST
..K..........V.K..P......EIA........L.Y.EKP.YQ.L..IL..G....G.....T
RetrocopyGSKLRYRENIAGLVDKCFPEKNKPDEIAKYMETVKLLDYTEKPHYQNLRDILLQGLKAIGSKDDGT

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_753 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 3 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000003299 1 retrocopy
retro_chof_753 ,
Choloepus hoffmanni ENSCHOG000000100803 retrocopies
Otolemur garnettii ENSOGAG000000160631 retrocopy



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