RetrogeneDB ID: retro_chof_1480

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_304011:505..1217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSCHOG00000012828
• Aliases: None
• Description: zinc finger, DHHC-type containing 6 [Source:HGNC Symbol;Acc:19160]

Sequence

>retro_chof_1480
CTTTCTTTTGAGTGGAACACAGTACAGACAGACATGAGTGCAGCCCAGGGTGATCCTCTTCTGGTTGTTCTGTTTGAATT
ATCTGCATTTGCTACCACTTTGTTTGCCTTGGGATCAGCTCTAAGAACAACCATAGCTGTTGGGATGTTGTTTTTCGTCC
AGATAAAAATAATTCCCAGAAACAAAGCATCCATTGAATCATGGATTGAAGAGAAGGCTAAAGATCTAATTCAATACTAT
CAACTAAATGAAGTCTTTGTTTTTCCTTATGATATGGAAAGTAGATGAAAGAATTTTACACAGGTATTTACATGCCAGGG
GCCCCTGAAGGAGATGGATTGGAGTGAATAGTAAGTGAAGTCTGCCACCAGTACAGTTTAACAATAGAACTGGTGAAACA
AAAATCACGTAAGAGAGTCAGGCGTTTTCACTATCAAGTAAAAGAAGAATACAGTGGTGCCTGCTGTCCTTTGAATAAAG
GAATCAAAACCTTGTTCACAAGCTCCTGCATTGAAGAGCCTCAAATAAGGCTACAGAAAAGGGAGTTCATTTTAGCCACA
AGAGTTTTACAATACTGGTTGTATGGAGACAAAATTGATGATTCCTTTTTAGAAGGTATTTCAAGAATAAGAGGAAGGTT
TCCTAGAAACTGTGTGAAAAGTGTCCCTGTGATGCTGAAAGAGATCAAGTCCCAGAGGGCAAGAAGAAAAAT

Alignment

ORF - retro_chof_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.63 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSFGWNTVKIDMSAARRDPLPIVPFGLAAFAATLFALGLALGTTIAVGMLFFIQXXXXXXXXXXXXXXXX
          LSF.WNTV..DMSAA..DPL..V.F.L.AFA.TLFALG.AL.TTIAVGMLFF.Q................
Retrocopy LSFEWNTVQTDMSAAQGDPLLVVLFELSAFATTLFALGSALRTTIAVGMLFFVQIKIIPRNKASIESWIE

Parental  XXAKDRIQYYQLDEVFVFPYDMESRWKNFKQVFTWSG-VPEGDGLEWPVREGCHQYSLTVEQLKQKADKR
          ..AKD.IQYYQL.EVFVFPYDMESR.KNF.QVFT..G..PEGDGLE..V.E.CHQYSLT.E..KQK..KR
Retrocopy EKAKDLIQYYQLNEVFVFPYDMESR*KNFTQVFTCQG<APEGDGLE*IVSEVCHQYSLTIELVKQKSRKR

Parental  VRSVRYKVIEDYGGACCPLNKGVKTFFTSPCTEEPRIRLQKGEFILAKRGLRYWLYGDKILDDSFIEGAS
          VR...Y.V.E.Y.GACCPLNKG.KT.FTS.C.EEP.IRLQK.EFILA.R.L.YWLYGDKI.DDSF.EG.S
Retrocopy VRRFHYQVKEEYSGACCPLNKGIKTLFTSSCIEEPQIRLQKREFILATRVLQYWLYGDKI-DDSFLEGIS

Parental  RIRGWFPRNCV-EKYPYDAETDQAQKSEKKN
          RIRG.FPRNCV.EK.P.DAE.DQ.....KKN
Retrocopy RIRGRFPRNCV<EKCPCDAERDQVPEGKKKN

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_1480 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480 ,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,