RetrogeneDB ID: retro_chof_2618

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_91207:5035..5542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR77
• Ensembl ID: ENSCHOG00000013829
• Aliases: None
• Description: WD repeat domain 77 [Source:HGNC Symbol;Acc:29652]

Sequence

>retro_chof_2618
GCTGTTGAATTGTGGGATGAGAATGAGACACTCATTGTCAGCAAGTTCTGCAAGTATGAGCACGATGATATTGTATCTAC
AGTCAGCGTCCTGAGCTCTGGCACACAAGCTGTCAGCGGTAGCAAAGACTTCTGCATTAAGGTTTGGGACCTTGTTCAAC
AGACAGTTCTGAACTCATACCGAGCTCACTCTGGGCAGGTCACCTGTGTTGCTGCCTCTCCCTGCAAGGACTCTGTATTT
CTTTCATGCAGTGAGGACAGTAGAATTTTACTCTGGGATACTCGTTCTTCCAAGCCGGCATCACAGTTGAGCTACACTGC
CTCTGGCTTTCTTCCTACCTAACTGGCTTGGCATCTTCAGCAAAGTGAAGCCTTTGTCTTTGGTGATGAGAATGGGACTG
TCTCCATTGTGGACACCAAAAATGCAAGCCTTGCCCTCAGCTCAACTGTGCACTCCCAGTGTGTCACTGGGCTGGTGTTC
TCGCCACACTATTCTGTTCCTGGCCTC

Alignment

ORF - retro_chof_2618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 70.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDFCIKVWDLVQQTVLNSYRAHSGQIT
          AVELW..DENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDFCIKVWDLVQQTVLNSYRAHSGQ.T
Retrocopy AVELW--DENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDFCIKVWDLVQQTVLNSYRAHSGQVT

Parental  CVAASPYKDSVFLSCSEESGNLFQNTCCPKLVS-IGYTASGFLPTSLAWHPQQSEAFVFGDENGTVSVVD
          CVAASP.KDSVFLSCSE.S..L...T...K..S...YTASGFLPT.LAWH.QQSEAFVFGDENGTVS.VD
Retrocopy CVAASPCKDSVFLSCSEDSRILLWDTRSSKPASQLSYTASGFLPT*LAWHLQQSEAFVFGDENGTVSIVD

Parental  TKNASLALSSAVHSQCVTGLVFSPH-SIPFL
          TKNASLALSS.VHSQCVTGLVFSPH.S.P.L
Retrocopy TKNASLALSSTVHSQCVTGLVFSPHYSVPGL

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_2618 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618 ,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166, retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,