RetrogeneDB ID: retro_chof_422

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_106621:3468..3728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50B
• Ensembl ID: ENSCHOG00000003928
• Aliases: None
• Description: transmembrane protein 50B [Source:HGNC Symbol;Acc:1280]

Sequence

>retro_chof_422
GTGATCAATACAATATCAAATCAAGTCTGAGGGAATAGTTACAGTGAAGGCTTCCGGGTCAAACAGGAGCTTGCATTTGG
CTGTTCATTGGTTTCATGTTGGCCTTTGGATATCTGATTGCATCTATGTGGATTCAGTTTGGAGGTTCTGTTGTTAAAGA
GAAACCCACAGTGTATCATGGAATTGCTGTATTTTTCCAGAATGCCTTCATCTTTTTTAGAGGACTGGTTTTTAAGTGTG
GCCGCACTGACTACTTATGG

Alignment

ORF - retro_chof_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.67 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MINAVSNAQVRGDSYESGCL-GRTGARVWLFIGFMLMFGSLIASMWILF-GAYVTQSIDVYPGLAVFFQN
          .IN..SN.QV.G.SY..G...G.TGA..WLFIGFML.FG.LIASMWI.F.G..V.....VY.G.AVFFQN
Retrocopy VINTISN-QV*GNSYSEGFR<GQTGACIWLFIGFMLAFGYLIASMWIQFGGSVVKEKPTVYHGIAVFFQN

Parental  ALIFFSTLIYKFGRTEELW
          A.IFF..L..K.GRT..LW
Retrocopy AFIFFRGLVFKCGRTDYLW

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_422 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
Choloepus hoffmanni	ENSCHOG00000003928	1 retrocopy	retro_chof_422 ,
Gorilla gorilla	ENSGGOG00000034844	1 retrocopy	retro_ggor_1487,
Myotis lucifugus	ENSMLUG00000012388	1 retrocopy	retro_mluc_970,
Nomascus leucogenys	ENSNLEG00000003887	1 retrocopy	retro_nleu_2077,
Pan troglodytes	ENSPTRG00000013869	1 retrocopy	retro_ptro_1379,
Ictidomys tridecemlineatus	ENSSTOG00000023740	1 retrocopy	retro_itri_678,