RetrogeneDB ID: retro_chof_202

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4429:21131..21632(+)
• Located in intron of: ENSCHOG00000005703

Retrocopy information

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

Parental gene information

• Parental gene symbol: VSTM5
• Ensembl ID: ENSCHOG00000010429
• Aliases: None
• Description: V-set and transmembrane domain containing 5 [Source:HGNC Symbol;Acc:34443]

Sequence

>retro_chof_202
CAGGGAGCATCACTGTACACTCCCCAGTCCATCATCAACGCTACAGTGGAAGAAGACATTCTGCTCTTGAATACTCCTCC
CATGGGGTGCCCACCATCGAATGGAAGTATACATCCAACTTGGGGTGTGCAGAAGATTGCGGAGTGGAAACCAGGGACTC
AGGCCAACATCTCACAAAGCCACAAGGACAGAATCTGCACCTTCAACAATGGCTCCATTCAGCTTTTCAGTGTGGGTGTG
AGAGATTCTGGCTACTATGTCATCACAGTGACTGAGCGCCTGGGGAGCAGTCAGTTTGGCACCATCGTGCTGCATGTATC
TGAGATCCTCTGTGAAGACCTCCACTTTGTCGCTGTCTTCCTTGCTTTGCTCACTGCTATGGCTGTTTGTTGATCAGCCC
CATGTGGGAGTGCAATGAGTGTGTATATGAAGTCCAGAGGAAGAGAAGACACACTCAAAGAAAGTACAACTGAGGAGACT
GAGCTGTCAGATGTTAAGTGT

Alignment

ORF - retro_chof_202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QGVSLYIPQSIINATVEEDILL-SVEYSCHGVPTIEWKYTSN-WGVQKIVEWKPGTQANISQSHKDRICT
          QG.SLY.PQSIINATV.E...L...EYS.HGVPTIEWKYTSN.WGVQKI.EWKPGTQANISQSHKDRICT
Retrocopy QGASLYTPQSIINATV-EEDIL<ALEYSSHGVPTIEWKYTSN>WGVQKIAEWKPGTQANISQSHKDRICT

Parental  FDNGSIQLFSVGVRDSGYYVITVTEHLGSSQFGTIVLHVSEILYEDLHFVAVFLALLAAVA-AVLISLMW
          F.NGSIQLFSVGVRDSGYYVITVTE.LGSSQFGTIVLHVSEIL.EDLHFVAVFLALL.A.A...LIS.MW
Retrocopy FNNGSIQLFSVGVRDSGYYVITVTERLGSSQFGTIVLHVSEILCEDLHFVAVFLALLTAMA<CLLISPMW

Parental  VCNKCVYKVQRKRRHKLKE-STTEEIELQDVEC
          .CN.CVY.VQRKRRH......T.E..EL.DV.C
Retrocopy ECNECVYEVQRKRRHTQRK>TTEE-TELSDVKC

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_202 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010429	1 retrocopy	retro_chof_202 ,