RetrogeneDB ID: retro_chof_1636

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_34757:6574..7684(-)
• 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_1636
AATTCCAAAACCCTGGCATTTCTCATTCTTGCTGTTGAACCCATTGTTAAGTTAAAATTCATGCCCAGGACTGGAACGTG
AGTTTTTATTCTCCCACCTAGTAGGGAACTGGCCATGCACACTTTTGGCGTGCTTAAGGAGCTAATGACTCATCATGTCC
ACACATATAGGTTGATAATGGGGGGCAGTGACAGATCTGTTGAAGCACAGAAACTTGCTAATGGGATCAATATCATGGTG
GCCACACCAGGTCAACTCCCTGACCATATGCAGAATACCCCGGGGTTTATGTATAAAAACCTGCAGTGTGTGGTTATTGA
TAAGGCCAATCATATCTTGGATGTTGGGTTTGAAGAGCAGTTAAAGCAAATTATTAAACTTCTGCCAGTAGGCAGACAGA
CCATGCTCTTTTCTGCCATGCAAACTCGAAAAGTTGAAGACCTAGCAAGAATTTCTCTAAAAAAAGAACCATTGTATGTT
GGTGTTAATGATGATAAAACTAATGAAACAGTGGATGGTCTTAAGCAGGGATATGTTGCTTGTCCCTCTGAAAAGAGATT
CCTTCTGCTATTCACATTCCTTAAGAAGAACTGAAAGAAGAAACTGATAGTGTTCTTTTCATCCTGTAAGTCCGTGAAAT
ACCACTATGAGTTGCTGAACTACATCGATTTGCCTGTCTTGGCCATTCATGGAAGGCAGAAACAAAATAAGCAGGCAACC
ACCTTCTTCCAGTTCTGCAGTGCAGATTTGGGAATACTGTTGTGTGCAGACGTGGCAGCTCGAGGGCTGGATACTCCTGA
AGTCAACTGGGTTGTTCAGTATGACTCTCCAGATGACCCTAAGTATACTGATCATGTGGGTAGAACAGCCAGAGGCCTGA
ATGGAAGAGGACATGCCTTGCTCATTTTGCAAGAAGAATTGGGTTTCCTTCACTACTTGAAGGGATCCAAGGTACCATGA
CATGAATTTGAGTTTTCCTGGTGCAAAATTTCTGACATTCAGTCTCAGTTTGAGAAATTGTTTGAAAAGAACTACTTCCT
TCATAAGTCAGCTCAGGAAGTATGTAAGTCATACATTCGAGCATATGATTCCCATTTTCTGAAACCTATA

Alignment

ORF - retro_chof_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 58.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGKTLAFLIPAIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQ
          ..KTLAFLI.A.E.IVKLKFMPR.GT.V.IL.P.RELAM.TFGVLKELMTHHVHTY.LIMGGS.RS.EAQ
Retrocopy NSKTLAFLILAVEPIVKLKFMPRTGT*VFILPPSRELAMHTFGVLKELMTHHVHTYRLIMGGSDRSVEAQ

Parental  KLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPVRRQTMLFSAT
          KL.NGINI.VATPG.L.DHMQNTPGFMYKNLQC.VID.A..ILDVGFEE.LKQIIKLLPV.RQTMLFSA.
Retrocopy KLANGINIMVATPGQLPDHMQNTPGFMYKNLQCVVIDKANHILDVGFEEQLKQIIKLLPVGRQTMLFSAM

Parental  QTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSEKRFLLLFTFPKKNRRKKMMVFFSSCK
          QTRKVEDLARISLKKEPLYVGV.DDKTN.TVDGL.QGYV.CPSEKRFLLLFTF.KKN..KK..VFFSSCK
Retrocopy QTRKVEDLARISLKKEPLYVGVNDDKTNETVDGLKQGYVACPSEKRFLLLFTFLKKN*KKKLIVFFSSCK

Parental  SVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDP
          SVKYHYELLNYIDLPVLAIHG.QKQNK..TTFFQFC.AD.G.LLC.DVAARGLD.PEV.W.VQYD.PDDP
Retrocopy SVKYHYELLNYIDLPVLAIHGRQKQNKQATTFFQFCSADLGILLCADVAARGLDTPEVNWVVQYDSPDDP

Parental  KEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFEFSWSKISDIQSQLEKLIEKNYFLH
          K.Y...VGRTARGLNGRGHALLIL..EELGFL.YLK.SKVP..EFEFSW.KISDIQSQ.EKL.EKNYFLH
Retrocopy K-YTDHVGRTARGLNGRGHALLILQ-EELGFLHYLKGSKVP*HEFEFSWCKISDIQSQFEKLFEKNYFLH

Parental  KSAQEAYKSYIRAYDSHSLKQI
          KSAQE..KSYIRAYDSH.LK.I
Retrocopy KSAQEVCKSYIRAYDSHFLKPI

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_1636 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 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,