RetrogeneDB ID: retro_chof_1283

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_249767:1218..1596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUS4L
• Ensembl ID: ENSCHOG00000006848
• Aliases: None
• Description: dihydrouridine synthase 4-like (S. cerevisiae) [Source:HGNC Symbol;Acc:21517]

Sequence

>retro_chof_1283
TATGCAAATAGAATATACATTAACTGTGGTTGCCCTCAGAGGTGGGCTGTGGCAGAAAGTTATGGGACTTGCTTAATAAA
TAAGCCAGAGCTTGTTTGGGGTATGATGAAATAAGTGAAAAATCAAGTGGAAAACCCCAGATACTCAGAATCTATTAAAA
TCATCCATGATGATCTTATAAGAACTACAGACTTTTGTTAAAAGGCTGAAGCAACATGAGTTTATTAGATTACAGTCCGT
GGAAGAAGTGTTGAAGAAAGAGATAAGCCCGTCCACTGTGATGCTATTAAAATAATTAAGGAAAATATGTCTCTACCTGT
AATTGCTAATGGAAATAGCAAGAGTTTAAAAGAAGCAGAAAATGTGTGTCAAATTACT

Alignment

ORF - retro_chof_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.65 %
• Parental protein coverage: 53.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YANGIDINCGCPQRWAMAEGYGACLINKPELIQDMVKQVKNQVENPRFSVSIKIRIHDDLTRTVDLCRKA
          YAN.I.INCGCPQRWA.AE.YG.CLINKPEL...M.K.VKNQVENPR.S.SIKI.IHDDL.RT.D.C.KA
Retrocopy YANRIYINCGCPQRWAVAESYGTCLINKPELVWGMMK*VKNQVENPRYSESIKI-IHDDLIRTTDFC*KA

Parental  EATGVSWITVHGRTVEERHQPVHYDAIKIIKENLSIPVIA-GDIKSLE--AHVWQIT
          EAT.V..ITV.GR.VEER..PVH.DAIKIIKEN.S.PVIA.G..KSL.....V.QIT
Retrocopy EAT*VY*ITVRGRSVEERDKPVHCDAIKIIKENMSLPVIANGNSKSLKEAENVCQIT

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_1283 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006848	1 retrocopy	retro_chof_1283 ,
Cavia porcellus	ENSCPOG00000002384	1 retrocopy	retro_cpor_701,
Otolemur garnettii	ENSOGAG00000013113	2 retrocopies	retro_ogar_1578, retro_ogar_894,