RetrogeneDB ID: retro_chof_1022

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_184930:2759..3054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D2
• Ensembl ID: ENSCHOG00000007821
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 2 [Source:HGNC Symbol;Acc:20328]

Sequence

>retro_chof_1022
CAGTTTGCTTTTAATTTTACAAATAATCTGGGACAAAAATGATCAGATCTAGAAACAGTCACTGCCTACTAGAATTTACT
GTTTAATGGAAGATTTAAATTCTTATACTTATGGAATAAATTTTTGTTGGAACACCATAAACAGTCGATACAGAAAGATA
TTGGAATCTTCTTTTAAAGTTAAGTACAATGAAAGCAGATGCCATGTCTAATGATGAAGCAGAGCATGCCATGTTCTTAT
TGATGACATTGTGGAATTTGCAAGTCCTCAAATTTCTGGAAGAAAAAGAACAACA

Alignment

ORF - retro_chof_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.8 %
• Parental protein coverage: 54.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QFTFTFAKNPGQKGLDLEMAVAYWNLVLSGRFKFLDLWNKFLLEHHKRSIPRDT-WNLLLDFGNMIADDM
          QF.F.F..N.GQK..DLE...AY.NL...GRFKFL.LWNKFLLEHHK.SI..D..WNLLL....M.AD.M
Retrocopy QFAFNFTNNLGQK*SDLETVTAY*NLLFNGRFKFLYLWNKFLLEHHKQSIQKDI<WNLLLKLSTMKADAM

Parental  SNYDE-EGAWPVLIDDFVEYARPVVKGGKHST
          SN.DE...A..VLIDD.VE.A.P...G.K..T
Retrocopy SN-DE<SRACHVLIDDIVEFASPQISGRKRTT

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_1022 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 4 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007821	4 retrocopies	retro_chof_1022 , retro_chof_1937, retro_chof_461, retro_chof_771,
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Mus musculus	ENSMUSG00000038506	1 retrocopy	retro_mmus_2204,
Pongo abelii	ENSPPYG00000005527	1 retrocopy	retro_pabe_2894,