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 symbol: VRK2
• Ensembl ID: ENSCHOG00000003299
• Aliases: None
• Description: vaccinia related kinase 2 [Source:HGNC Symbol;Acc:12719]

Sequence

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

Alignment

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:

Parental  NDARHVIKVEYQENGPLFSELKFYQRAAKKEYIKRWIALKQLDYLGIPLFYGSGLTTFKGRSYRFMVMER
          .DA..V.K.E...NG.L..ELKFYQRAAK.E.I..WI....L.YLG.P...GSGL....G.SYRFM.M.R
Retrocopy SDAPCVVKAEPSGNGLLITELKFYQRAAKPEQIQKWIHSHKLKYLGVPKYWGSGLHDKNGKSYRFMIMDR

Parental  LGKDLQKISDQNGT-FKKSTVLHLGIRMLDVLEYIHENEYIHGDIKAANLLLGYKNPEQVYLADYGLSYR
          .G.D.QKI...N...F...TVL.L..R.LD.LEYIHE.EY.HGDIKA.NLLL.YKNP.QVYL.DYGL..R
Retrocopy FGSDRQKIYEANAKRFSQKTVLKLSLRILDILEYIHEHEYVHGDIKASNLLLSYKNPDQVYLVDYGLADR

Parental  YCPN-GNHKEYQENPRKGHNGTIETSLD-AHKGVALSRRSDLEILGYCMLRWLCGKLPWERNLKDPVAVQ
          YCP..G.HKEY.E.P...H.GT.E......H.GVA.SRR.DLEILGYCM..WL.G.LPWE.NLKDP..V.
Retrocopy YCPE>GVHKEYKEDPKRCHDGTLEFTST>MHNGVAPSRRGDLEILGYCMIWWLSGCLPWEDNLKDPNYVR

Parental  TAKTNLLDELPESVFKWAPSGSSCYEIAQFLACAHSLAYDEKPDYQILKKILNPGGIPLGPLEFST
          ..K..........V.K..P......EIA........L.Y.EKP.YQ.L..IL..G....G.....T
Retrocopy GSKLRYRENIAGLVDKCFPEKNKPDEIAKYMETVKLLDYTEKPHYQNLRDILLQGLKAIGSKDDGT

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_753 was not experimentally validated.

Homology

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	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058, retro_chof_216,
Otolemur garnettii	ENSOGAG00000016063	1 retrocopy	retro_ogar_47,