RetrogeneDB ID: retro_chof_1539

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31773:12498..13628(-)
• 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_1539
GATCTTCTAGTGGCTGCAAAAACAGGCAGTGGCAAAACTCGGGCATTTCTCATCCTTGTTGTTGAACTCATTGTTAAGTT
AAAATTCATGCCCAAGAATGGAACAGGACTCCTTATTATCTCACCTACTAGGAAAATGGCCATGCAGACATTTGGTGTGC
TTAAGGAACTAATGAAACCATGTCCACACAAACGGTTTGATTATGGAGGGCAGTAGCAGATTTGCTGAAGCACAGAAACT
TGGTAATGGGATCAACACCAGTGTGGCCACACTAAGTTGACTTCCAGACCATACGCAGAATACCCCAGGGTTTATGTATA
AAAATCTACAGTGTCTGGTATTGATGAGGTTGATTGTATCTTGGACGTTGAGTTTGAAGAGGATTAAAGCAAATAATTAA
GCTTCTGCCAATAAGTAGACAGACCATGCTCTTTTCTGCCATGTAAACTCTAAAAGTTGAAGAGCTGGAAAGAATTTCTC
TGAAGAATGAACCACTGTATATTGGTGTTGATGATAAAACTAATGCAACAGTTCATTGTCTTCAGCAGGAATGCATTGTT
TGTCCCTCTGAAAAAAAGATTTCTTCTGCTTTTTACATTCCTTTAGAAGAACTGAAAGAAGAAAATGATGGTGTACTTTT
CATTCTGTAAGTCCATGAAATACCGCTACAAGTTTCTGAACCACATTTATTTGCCTGTCTTGGCCATTCATGGAAGGCAG
ACGCAAAATAAGCAGACAACCTTTTTCCAGTTCTGCAACACAAATTCGGAGATACCATTGGGTATAGACATGGCAGTTCA
AGGACTGGCTATCCCTGAAGTTGACTGGATTGTTCAGGATGACCCTCCAGATGACCCTAAAGAAGGTATTCGTCATGTGG
GTAGAACAGCCAGAGGCCTAAATGGAAGAGGACATGCCTTGCCCATTTTGCTGCCTAGGGGAGAATTGTGTTTCCTTCAT
TAATTGAAGCAATCAAGGGCTCCATTAAGTGAATTTGAGTTTTCCTGGCCCCAATTTTTGACATTCATTCTCAGCTTGAG
AAATTGATTGGAAAACAAAACAAAACAAAACAGAAAAAAACTACTTCTTTCATAAATCAGTCCAGGAAGTGTGTAAGTCA
TACATTCAAG

Alignment

ORF - retro_chof_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 59.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DLLAAAKTGSGKTLAFLIPAIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELM-THHVHTYGLIM
          DLL.AAKTGSGKT.AFLI...ELIVKLKFMP.NGTG.LI.SPTR..AMQTFGVLKELM..H.VHT.GLIM
Retrocopy DLLVAAKTGSGKTRAFLILVVELIVKLKFMPKNGTGLLIISPTRKMAMQTFGVLKELM>NH-VHTNGLIM

Parental  GGSNRSAEAQKLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLV-IDEADRILDVGFEEE-LKQIIKLL
          .GS.R.AEAQKL.NGIN..VAT...L.DH.QNTPGFMYKNLQCLV.IDE.D.ILDV.FEE..LKQIIKLL
Retrocopy EGSSRFAEAQKLGNGINTSVATLS*LPDHTQNTPGFMYKNLQCLV<IDEVDCILDVEFEED<LKQIIKLL

Parental  PVRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSE-KRFLLLFTFPKKN
          P..RQTMLFSA..T.KVE.L.RISLK.EPLY.GV.DDKTNATV..L.Q...VCPSE.KRFLLLFTF..KN
Retrocopy PISRQTMLFSAM*TLKVEELERISLKNEPLYIGV-DDKTNATVHCLQQECIVCPSE>KRFLLLFTFL*KN

Parental  RRKKMMVFFSSCKSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPE
          ..KKMMV.FS.CKS.KY.Y..LN.I.LPVLAIHG.Q.QNK..TTFFQFCN..S...L..D.A..GL.IPE
Retrocopy *KKKMMVYFSFCKSMKYRYKFLNHIYLPVLAIHGRQTQNKQ-TTFFQFCNTNSEIPLGIDMAVQGLAIPE

Parental  VDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPE-ELGFLRYLKQSKVPLSEFEFSW-SKISDI
          VDWIVQ.DPPDDPKE.I..VGRTARGLNGRGHAL.IL.P..EL.FL..LKQS..PLSEFEFSW...I.DI
Retrocopy VDWIVQDDPPDDPKEGIRHVGRTARGLNGRGHALPILLPRGELCFLH*LKQSRAPLSEFEFSW<APIFDI

Parental  QSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLK
          .SQLEKLI..................R...SH..K
Retrocopy HSQLEKLIXXXXXXXXXXXTSFINQSRKCVSHTFK

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_1539 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,