RetrogeneDB ID: retro_chof_2100

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_491:31203..32846(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITCH
• Ensembl ID: ENSCHOG00000011115
• Aliases: None
• Description: itchy E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:13890]

Sequence

>retro_chof_2100
GAATCTGTTCGGCAACAGACTGGAAATGCCAACACAGAAACTTTGCCATCAAGTTGGGAAAGAAGAGCTGATGATCATGG
AAGAGCTTATTAGTGGACCATAATACCAGAACAGCAACATGGCAGTGACCCAACATGGAATCTGTCTGAAACTTGGAACA
GTGGCCATCTCAGCAGAACCAGTTACAGGCAGCTATGCAATAGTTCAACCAGTGATACCTCTATTTCGCTTCAATGTTAG
CTGCAGAAAACAACCCATATGGGCCTTTGCCAACAAGCTGGGAAAAAAGAGTGGATTCCACAAACGGGGTTTAAAATCAT
AACACAAAAACAACGCAATGGGACGATCCAAGAACTCAAGGCCTACAGAATGAGAACCCCTGCCAGAACCTGGGAAATTA
GGTACACTTTAGAAGGTGTTAGGTACTTTGTTGAACATAAAGCAAGAACAACAACATTCAAAGATCCTCGCAATGGGAAG
TCATCTGTAATGAAAGTTGGTCCACAAATTGCTTATGAATGCAGCTTTGGGTAGAAACTTGCTCATTTCTGTTATTTGTG
CCAGTCTAATGCACTGCCCAGTCATGTGAAGATCAGTGTGTCCTGGCAGACAGTGTTGGAAGATTCCTTCCAACAGATTA
TGGCATTAAAACCATATGACTTGAGGAGGAGATTATATGTAATATTAAGAGGAGAAGGACTTGATTATGGTGGTCTAGCA
AGAGAATAATTTTTCTTACTTTCACATGAAGTTTTGAACCCAATGTATTGTTTATTTGAGTATGCTGGCAAGAACAGCTA
CTCCCTGCAGATAAATCCGGCATCAACCATTAATCCAGATCATCTTTCATACTTTTGCTTCATTGGTTGCTTTATCACTG
TGGCACTTTTTTGTAGAAAGTTTATTGATACTGGTTTCTCTTTACCATTCTACAAGTGTTTGCTAAGTAAAAAATTTACT
GTTAAGGAATTGGAATCAATTGATACTGAATTTTATAACTCCCTTATCTGGATAAGAGACAATAATATTGAATAATGTGG
TTTAGAAATGTACTTTTCTGTTGACATGGAGATTCTGGGAAAGGTTACTTCACGTAACCTGAAATTGGGAGGTTCCAATA
TTCTGGTGACTGAAGAGAACAAAGATGAATATATTGGTTTAATGACAGAATGACATTTTTCTCAAGGAGTACAAGAACAG
ACCAAAGCTTTCCTTGATGGTTTTAATGAAGTTGTTCTCCTTCAATGGCTGCAGTACTTTGATGAAAAGGAATTAGAGGT
TATGTTGTGTGGCATGCAGGAGACTAACTTGGCAGATTGGCAGAGAAACACTGTTTATTGGCATTATACAAGAAACAGCA
AGCAAATAATTTGGTTTTGGCAGTTTGTGAAAGACAATGAAGTAAGAATGTGACTACTGCAGTTTGTCACTGGAACCTGC
TGTTTACCTCTAGGAGGGTTTGCTGAGCTCATGGGAAGTAATGGGTCTCAAAAATTTTGCATAGAAAAAGTTGGCAAAGA
CACCTGGTTACCAAGAAGTCACATGTGTTTTAATTGCTTGGATCTACCACCATATAAGAGTTATGAACAACTAAAGGAAA
AGCTTCTTTTTGCAATAGAAAGACAGAGGGATTTGGACAAGAA

Alignment

ORF - retro_chof_2100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.01 %
• Parental protein coverage: 63.34 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DHVEKRTTWDRPEPLPPGWERRVDNMGRIY-YVDHFTRTTTWQRPTLESVRNYEQWQLQRSQLQGAMQQF
          ..V...T.....E.LP..WERR.D..GR.Y..VDH.TRT.TWQ.P..ESV.N.EQW..Q..QLQ.AMQ.F
Retrocopy ESVRQQTGNANTETLPSSWERRADDHGRAY<LVDHNTRTATWQ*PNMESV*NLEQWPSQQNQLQAAMQ*F

Parental  NQRFIYGNQDLFATPQSKEFDPLGPLPPGWEKRTDSNGRVYFVNHNTRITQWEDPRSQGQLNE-KPLPE-
          NQ...Y....L.A........PL...P..WEKR.DS...V...NHNT..TQW.DPR.QG..NE..PLPE.
Retrocopy NQ*YLYFASMLAA--ENNPYGPL---PTSWEKRVDSTNGV--*NHNTKTTQWDDPRTQGLQNE<EPLPE<

Parental  GWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSA-LDNGPQIAYVRDFKAKVQYFRFWCQQLIVPQHIKIT
          .WE.R.T..G..YFV.H..RTTT..DPR.GKS.....GPQIAY...F..K...F...CQ....P.H.KI.
Retrocopy TWEIRYTLEGVRYFVEHKARTTTFKDPRNGKSSVMKVGPQIAYECSFG*KLAHFCYLCQSNALPSHVKIS

Parental  VTRKTLFEDSFQQIMSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVLNPMYCLFEYAGKDNYC
          V...T..EDSFQQIM...P.DLRRRL.VI..G.EGLDYGG.ARE.FFLLSHEVLNPMYCLFEYAGK..Y.
Retrocopy VSWQTVLEDSFQQIMALKPYDLRRRLYVILRG-EGLDYGGLARE*FFLLSHEVLNPMYCLFEYAGKNSYS

Parental  LQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNKPVGLKDLESVDPEFYNSLIWV
          LQINPAS.INPDHL.YF.FIG.FI..ALF..KFIDTGFSLPFYK..L.K....K.LES.D.EFYNSLIW.
Retrocopy LQINPASTINPDHLSYFCFIGCFITVALFCRKFIDTGFSLPFYKCLLSKKFTVKELESIDTEFYNSLIWI

Parental  KENNIEECGLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWRLSRGVEEQTQAFFEGF
          ..NNIE.CGLEMYFSVD.EILG...S..LK..G.NILVTEENK.EYI....E...S.GV.EQT.AF..GF
Retrocopy RDNNIE*CGLEMYFSVDMEILGKVTSRNLKLGGSNILVTEENKDEYIGLMTE*HFSQGVQEQTKAFLDGF

Parental  NEILPQLYLQYFDAKELEVLLCGMQEIDLNDWQRHTIYRHYTRTSKQIMWFWQFVKEIDNEKRMRLLQFV
          NE......LQYFD.KELEV.LCGMQE..L.DWQR.T.Y.HYTR.SKQI.WFWQFVK..DNE.RM.LLQFV
Retrocopy NEVVLLQWLQYFDEKELEVMLCGMQETNLADWQRNTVYWHYTRNSKQIIWFWQFVK--DNEVRM*LLQFV

Parental  TGTCRLPVGGFADLMGSNGPQKFCIEKVGKENWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIE-ETEGF
          TGTC.LP.GGFA.LMGSNG.QKFCIEKVGK..WLPRSH.CFN.LDLPPYKSYEQLKEKLLFAIE..TEGF
Retrocopy TGTCCLPLGGFAELMGSNGSQKFCIEKVGKDTWLPRSHMCFNCLDLPPYKSYEQLKEKLLFAIE<KTEGF

Parental  GQE
          GQE
Retrocopy GQE

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_2100 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000308	1 retrocopy	retro_btau_1692,
Choloepus hoffmanni	ENSCHOG00000011115	1 retrocopy	retro_chof_2100 ,
Felis catus	ENSFCAG00000008780	1 retrocopy	retro_fcat_899,