RetrogeneDB ID: retro_chof_461

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_111991:2877..3245(-)
• 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_461
TCCATTAGTGTGATGATTACTGCATGGAAGTTCAGAGAAACAACAAAGTGTGACTTCTTCAAACAGAAATTCACATATTG
CATAATGGAATTATGAGGGGCAGCATAGAAAAATCAATGTACCTGTTACCCAAGATGGAACAAGAATTGAAAGAACCAGT
GTAATTTAAGGATTTTTACCAGTTTACTTTTAATTTTACAAAGAATCCAGGACAAAAAATTCTAGAAATAGCCATTGCCT
ACTGGAGTTTAATGCTTAATTCAAAATTTAAATTCTTAGACTTATGAAATAAGTTTTTATTGGAACAGCATAAATGATCA
TTACTGAAAGATACTTGCAATCTTTTGGACTTCAGTACAATGATTGCA

Alignment

ORF - retro_chof_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 67.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SISVLVIAWKFRAATQCEFSKKEFVDGMTEL-GCDSTEKLKLLPR-LEQELKDTVKFKDFYQFTFTFAKN
          SISV...AWKFR..T.C.F.K..F.....EL.G..........PR..EQELK..V.FKDFYQFTF.F.KN
Retrocopy SISVMITAWKFRETTKCDFFKQKFTYCIMEL*GAA*KNQCTCYPR<MEQELKEPV*FKDFYQFTFNFTKN

Parental  PGQKGLDLEMAVAYWNLVLSGRFKFLDLWNKFLLEHHKRSIPRDTWNLLLDFGNMIA
          PGQK...LE.A.AYW.L.L...FKFLDL.NKFLLE.HK.S...DT.N.LLDF..MIA
Retrocopy PGQK--ILEIAIAYWSLMLNSKFKFLDL*NKFLLEQHK*SLLKDTCN-LLDFSTMIA

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_461 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,