RetrogeneDB ID: retro_chof_409

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_104896:719..1129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABL5
• Ensembl ID: ENSCHOG00000012225
• Aliases: None
• Description: RAB, member RAS oncogene family-like 5 [Source:HGNC Symbol;Acc:21895]

Sequence

>retro_chof_409
ACCCGCCCAAACAAAAGCTCAGCGAGTGAATTTGAGCTGTGGGATTGTGGCTGTGATCCAAAGTTGGATCTTGCTGGCTG
GCCCTGATGAAGGACTCTCATGAAGTGGCTGTTATCTTCAATGCTGACATCCCAAGGCGCCTGAAGGAAACTGAGATGTG
GTACTCCTACCTTGTTCAGCAGCATCTATTACAGGATAATCAGTGTCTATTAATTGTGCATCACAAACTAGGCTTTGGAG
GTGATAAAGGAAATCGGCCTTTACCACCACTCTTGAACAAGCTGAAGCTGGTAACCTTGAATCTTCAGGATGACCCTGAA
GAGATCCAGATAGAATTCATCAAGTATTTTAAAAGCATAGTCAACTCAGTATCTGAGAGCAGAGACCAGGAGGAGATGTC
AGTTATTACC

Alignment

ORF - retro_chof_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.19 %
• Parental protein coverage: 74.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSNNKGSGYEFELWDCGGDRKFE-SCWPALMKDAHGVAIIFNTDIPSHLKEIEMWYSCFVQQQLLQDNQC
          T..NK.S..EFELWDCG.D.K...SCW.ALMKD.H.VA.IFN.DIP..LKE.EMWYS..VQQ.LLQDNQC
Retrocopy TRPNKSSASEFELWDCGCDPKLD<SCWLALMKDSHEVAVIFNADIPRRLKETEMWYSYLVQQHLLQDNQC

Parental  LLIAHHKPGSGGDKGNLSLPPPLNKLKLVHSNLEDDPEEIRMEFIKYLKSVVNSVSETRDREEMSIIT
          LLI.HHK.G.GGDKGN..LPP.LNKLKLV..NL.DDPEEI..EFIKY.KS.VNSVSE.RD.EEMS.IT
Retrocopy LLIVHHKLGFGGDKGNRPLPPLLNKLKLVTLNLQDDPEEIQIEFIKYFKSIVNSVSESRDQEEMSVIT

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_409 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014343	1 retrocopy	retro_btau_1408,
Choloepus hoffmanni	ENSCHOG00000012225	1 retrocopy	retro_chof_409 ,
Macropus eugenii	ENSMEUG00000006225	1 retrocopy	retro_meug_331,
Myotis lucifugus	ENSMLUG00000012634	1 retrocopy	retro_mluc_2510,
Oryctolagus cuniculus	ENSOCUG00000007709	1 retrocopy	retro_ocun_522,
Tursiops truncatus	ENSTTRG00000005871	1 retrocopy	retro_ttru_110,