RetrogeneDB ID: retro_chof_2442

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_75801:4734..4965(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SVIP
• Ensembl ID: ENSCHOG00000013152
• Aliases: None
• Description: small VCP/p97-interacting protein [Source:HGNC Symbol;Acc:25238]

Sequence

>retro_chof_2442
ATGGGGTTTTATTTTCCCTGCCTCATGGAGGCTAAGCCTCCATCGCTGGACCCAGAAGAGAAAAAAGCATAACTTGCAGA
AGCTGCAGAGAGAAGAAAAGGGGAGGCTGAATTTCAGGACATTTTGGATGTTCAATCTGTGGAAGAAAAGAGAAAGCAAA
AGGAAAAATTAGGAAAACAAATCTCTACATCTGGAACCCCACTGGAAGGTGGACTTAGGTGGACAGTTTCA

Alignment

ORF - retro_chof_2442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLCFPCPGEAEPPSPDPEEKRAKLAEAAERRQREAASRGILDVQSVEEKRKKKEKLEKQIATSGLPPEG
          MG..FPC..EA.PPS.DPEEK.A.LAEAAERR..EA....ILDVQSVEEKRK.KEKL.KQI.TSG.P.EG
Retrocopy MGFYFPCLMEAKPPSLDPEEKKA*LAEAAERRKGEAEFQDILDVQSVEEKRKQKEKLGKQISTSGTPLEG

Parental  GLRWTVS
          GLRWTVS
Retrocopy GLRWTVS

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_2442 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013152	4 retrocopies	retro_chof_1571, retro_chof_2005, retro_chof_2442 , retro_chof_668,
Dasypus novemcinctus	ENSDNOG00000016735	4 retrocopies	retro_dnov_2035, retro_dnov_2072, retro_dnov_928, retro_dnov_945,
Sus scrofa	ENSSSCG00000022838	1 retrocopy	retro_sscr_446,