RetrogeneDB ID: retro_chof_870

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_159065:6293..6797(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WSB2
• Ensembl ID: ENSCHOG00000003651
• Aliases: None
• Description: WD repeat and SOCS box containing 2 [Source:HGNC Symbol;Acc:19222]

Sequence

>retro_chof_870
TTGGTTTCTGCATCCTGTGATAAGACTCTTCACATCTGGGACCTGAATAAACATGGTAAGCAGATTCAGGTGTTATCAGA
CCACCTGCAGTGGGTTAACTACTGCTCCATCTTGCCACAGGGCAGCACACTGTGCTCTGCAGCTGGAGAGAAGTCTGTCT
TTCTAGAGAGAATGTAGTCCTACATATTAATCCAGAAGCTAGAGGCCACCAAAGCAGTGTTGTCTTTTGTGACTTCTCCG
CGGACTCTGCCTTGCTTGTCACAGCTTCTTATGTGGTTATGTAGAACCCCTACACTGGCAAAAGGCTGAGGTCACTTCAC
CACACCATACCTCGACCCCACCATGGACAACAGTGATATCCACATTAGTTCACTGAGTTTGGTGTGCTTCTCTCCTGAAG
GCTTGTACCTTGCTATGGTGGCAGATGACAGCCTGCTCACGATCTGGGCCCTGGAACTGAAAACTCCAACCGCATTTGCT
CCTATGACCAATGGTCTCTGCTGC

Alignment

ORF - retro_chof_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.19 %
• Parental protein coverage: 57.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVSASRDKTLRIWDLNKHGKQIQVLSGHLQWVYCCSISPDCSMLCSAAGEKSVFLWSMRSYTLIRKLE-G
          LVSAS.DKTL.IWDLNKHGKQIQVLS.HLQWV..CSI.P..S.LCSAAGEKSVFL..M.SY.LI.KLE.G
Retrocopy LVSASCDKTLHIWDLNKHGKQIQVLSDHLQWVNYCSILPQGSTLCSAAGEKSVFLERM*SYILIQKLE<G

Parental  HQSSVVSCDFSPDSALLVTASYDTNVIMWDPYTGERLRSLHHA-QLDPPMDDSDVHISSLRSVCFSPEGL
          HQSSVV.CDFS.DSALLVTASY...V.M..PYTG.RLRSLHH...LDP.MD.SD.HISSL..VCFSPEGL
Retrocopy HQSSVVFCDFSADSALLVTASY---VVM*NPYTGKRLRSLHHT>YLDPTMDNSDIHISSLSLVCFSPEGL

Parental  YLATVADDRLLRIWALELKTPIAFAPMTNGLCC
          YLA.VADD.LL.IWALELKTP.AFAPMTNGLCC
Retrocopy YLAMVADDSLLTIWALELKTPTAFAPMTNGLCC

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_870 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.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003651	1 retrocopy	retro_chof_870 ,
Echinops telfairi	ENSETEG00000018534	2 retrocopies	retro_etel_1750, retro_etel_2174,
Microcebus murinus	ENSMICG00000005913	1 retrocopy	retro_mmur_1573,
Myotis lucifugus	ENSMLUG00000002114	1 retrocopy	retro_mluc_2097,
Macaca mulatta	ENSMMUG00000010236	1 retrocopy	retro_mmul_1466,
Mus musculus	ENSMUSG00000029364	1 retrocopy	retro_mmus_810,