RetrogeneDB ID: retro_chof_771

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_146486:1075..1551(-)
• 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_771
AGGCAGTTCTGTGATGCCCGGGACTCAATGCTGTCAGCATTTAGTGTCTTGGTCATTGCATGGAAGGTCAGAGAAGCAAC
GCACTGTGAGTTCGCCATACAGGAGCTCATAGATGGCATGACAGAATTAGTATGTGGCAGCAGAGAAAAACCAAAGGGCC
CAATACCCAAGATGGAACAAGAATCAAAAGAACCAGAACAATTAAAGGATTTTTACCAGTTTACTTTTAATTTACAAGGA
ATCAAGGACAAAAGGGACTAGATCTAGAAATGGCCACTGCCATTTAGTGAAATTTACTGTTTAAAGGAAATTTTAAATTC
TTAGATTTATGGAATAAAATTTTGTTGGAACATCATAAATAACCAATATGGAAAGATACTTTGAATATTCTTTTAGACTT
CAGTACAATGTTTGCAGATGACATATCTAATTATGATGAAGGAGTAATAGCAGTATGGCCTGTTTCTATTGATGAC

Alignment

ORF - retro_chof_771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.62 %
• Parental protein coverage: 84.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQFCDDLSLDPASISVLVIAWKFRAATQCEFSKKEFVDGMTELGCDSTEKLK-LLPRLEQELKDTVKFKD
          .QFCD.........SVLVIAWK.R.AT.CEF...E..DGMTEL.C.S.EK.K...P..EQE.K.....KD
Retrocopy RQFCDARDSMLSAFSVLVIAWKVREATHCEFAIQELIDGMTELVCGSREKPKGPIPKMEQESKEPEQLKD

Parental  FYQFTFT-FAKNPGQKGLDLEMAVAYW-NLVLSGRFKFLDLWNKFLLEHHKRSIPRDTWNLLLDFGNMIA
          FYQFTF..F..N.GQKGLDLEMA.A...NL...G.FKFLDLWNK.LLEHHK..I..DT.N.LLDF..M.A
Retrocopy FYQFTFN<FTRNQGQKGLDLEMATAI**NLLFKGNFKFLDLWNKILLEHHK*PIWKDTLNILLDFSTMFA

Parental  DDMSNYDEE--GAWPVLIDD
          DD.SNYDE.....WPV.IDD
Retrocopy DDISNYDEGVIAVWPVSIDD

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_771 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,