RetrogeneDB ID: retro_chof_64

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1031:20170..20471(-)
• Located in intron of: ENSCHOG00000003298

Retrocopy information

• Ensembl ID: ENSCHOG00000003330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB4A
• Ensembl ID: ENSCHOG00000013866
• Aliases: None
• Description: RAB4A, member RAS oncogene family [Source:HGNC Symbol;Acc:9781]

Sequence

>retro_chof_64
GAATGGAATTTAAAGATAATAAATGTTGGTGGTTAAATATATAAAGGTACAAATATAGGATATAGCAGGACAAGAACATT
TCAAGTCTGTGACAAGAAGTTATTACAGAGGGGCAGCAAGGGCTCTCCTTGTGTATGACATTACCAGCCGAGAAACCTAC
AATGTGCTTACTAAGTGGTTAACAGATGCCAGAATGCTAGCAAGTCAAAACACTGTGATTATCTTCTGCGGAAACAAGAA
GGATCTGGATGCAGATTGTGAAGTTACTTTCTTAGAGGCCTCCAGATTCGCTCAAGAAAGT

Alignment

ORF - retro_chof_64 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 72.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFGSKIINVGG-KYVKLQIWDTAGQERFRSVTRSYYRG-ARALLVYDITSRETYNALTNWLTDARMLASQ
          E...KIINVGG.KY.K.QI.D.AGQE.F.SVTRSYYRG.ARALLVYDITSRETYN.LT.WLTDARMLASQ
Retrocopy EWNLKIINVGG>KYIKVQI*DIAGQEHFKSVTRSYYRGAARALLVYDITSRETYNVLTKWLTDARMLASQ

Parental  NIVIILCGNKKDLDADREVTFLEASRFAQEN
          N.VII.CGNKKDLDAD.EVTFLEASRFAQE.
Retrocopy NTVIIFCGNKKDLDADCEVTFLEASRFAQES

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_64 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64 , retro_chof_703,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062,
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,