RetrogeneDB ID: retro_chof_2416

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_73492:745..1709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSCHOG00000004191
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_chof_2416
GATCTTCTAGCAGCTGGGAAAACAGGCAGTGGCAAAACCCTGGCCTTTCTCATCCCTGCTGTTGAACTCATTGTTAAGTG
AAAATTCATGCCCAGGAATGGAACAGGAAGAGTCCTTATTCTCTCACCTACTAGGGAGCTGGCCATGCTAACATTTGGTG
TGCTAAAGGAGCTAATGACCCACCACATCCACACATATGGGTTGATAATGGGGGGCAGTAACAGATCTGTTGAAGCACAG
AAACTTGCTAATGGGATCAACATCATTGTGGCCATACCAGGTGGACTCCTGGACCATATGCAGAATACCCCAGGGTTTTT
GTATAAAAACCTACAGGTCTTGTTACTGATGAGGCTGATCGTATATTGGATGTTGGGTTTGAAGAGGAATTAAAGCAAAT
TATTAAACTTCTGCCAGTATGCAGACGGATCATGCTATTTTCTGCCACACAAACTCTTAAAGTTGAAGACCTGGCAAGAA
TTTCTCTGAAAAAGGAGCCATTCTATGTTGGTGTTGATGATGATAAAACTAATGCAACAGTGGATGGGCTTGAGCAGGGA
TATGTTGTTTGTCACTCTGAAAAGAGATTCCTTCTGTTCTTTACATTCCTTAAGAAGAACCAAAAGAAGAAAATGAAGGT
ATTCTTTTCATCCTGAAAGTCTGTGAAATACCACTATGAGTTGCTGAACTACATCAATTTGCCTGTCTTGGACATTCATG
GAAAACAGAAGCAAAATAAGTGGACAACCACCTTCTTCCAGTTCTGCAATGCAGATTTGGGGATACTGTTGTGTACAGAC
ATGGCAGTTTGAGGGATGGATATTCCTGAAGTCGACTGGATTGTTCAGTATTACCCTCCAGATGACCCTACGGAATCTAT
TCGCCATGTGGGTAGAACAGCCAGAGGCCTATCTGGAAGAGGACATGACTTGCTCGTTTGCACCCAGATAATTTGGATTT
TCTT

Alignment

ORF - retro_chof_2416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 50.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLLAAAKTGSGKTLAFLIPAIELIVKLKFMPRNGTG-VLILSPTRELAMQTFGVLKELMTHHVHTYGLIM
          DLLAA.KTGSGKTLAFLIPA.ELIVK.KFMPRNGTG.VLILSPTRELAM.TFGVLKELMTHH.HTYGLIM
Retrocopy DLLAAGKTGSGKTLAFLIPAVELIVK*KFMPRNGTGRVLILSPTRELAMLTFGVLKELMTHHIHTYGLIM

Parental  GGSNRSAEAQKLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVI-DEADRILDVGFEEELKQIIKLLP
          GGSNRS.EAQKL.NGINIIVA.PG.LLDHMQNTPGF.YKNLQ.L...DEADRILDVGFEEELKQIIKLLP
Retrocopy GGSNRSVEAQKLANGINIIVAIPGGLLDHMQNTPGFLYKNLQVLLL<DEADRILDVGFEEELKQIIKLLP

Parental  VRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSEKRFLLLFTFPKKNRR
          V.R..MLFSATQT.KVEDLARISLKKEP.YVGVDDDKTNATVDGLEQGYVVC.SEKRFLL.FTF.KKN..
Retrocopy VCRRIMLFSATQTLKVEDLARISLKKEPFYVGVDDDKTNATVDGLEQGYVVCHSEKRFLLFFTFLKKNQK

Parental  KKMMVFFSSCKSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVD
          KKM.VFFSS.KSVKYHYELLNYI.LPVL.IHGKQKQNK.TTTFFQFCNAD.G.LLCTD.A..G.DIPEVD
Retrocopy KKMKVFFSS*KSVKYHYELLNYINLPVLDIHGKQKQNKWTTTFFQFCNADLGILLCTDMAV*GMDIPEVD

Parental  WIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLI-LRPEELGFL
          WIVQY.PPDDP.E.I..VGRTARGL.GRGH.LL..L.P..L.FL
Retrocopy WIVQYYPPDDPTESIRHVGRTARGLSGRGHDLLV<LHPDNLDFL

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_2416 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221, retro_chof_1539, retro_chof_1636, retro_chof_2416 , retro_chof_2418, retro_chof_721,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039,