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 summary: | ||
| Parental gene symbol: | ITCH | ||
| Ensembl ID: | ENSCHOG00000011115 | ||
| Aliases: | None | ||
| Description: | itchy E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:13890] |
Retrocopy-Parental alignment summary:
>retro_chof_2100
GAATCTGTTCGGCAACAGACTGGAAATGCCAACACAGAAACTTTGCCATCAAGTTGGGAAAGAAGAGCTGATGATCATGG
AAGAGCTTATTAGTGGACCATAATACCAGAACAGCAACATGGCAGTGACCCAACATGGAATCTGTCTGAAACTTGGAACA
GTGGCCATCTCAGCAGAACCAGTTACAGGCAGCTATGCAATAGTTCAACCAGTGATACCTCTATTTCGCTTCAATGTTAG
CTGCAGAAAACAACCCATATGGGCCTTTGCCAACAAGCTGGGAAAAAAGAGTGGATTCCACAAACGGGGTTTAAAATCAT
AACACAAAAACAACGCAATGGGACGATCCAAGAACTCAAGGCCTACAGAATGAGAACCCCTGCCAGAACCTGGGAAATTA
GGTACACTTTAGAAGGTGTTAGGTACTTTGTTGAACATAAAGCAAGAACAACAACATTCAAAGATCCTCGCAATGGGAAG
TCATCTGTAATGAAAGTTGGTCCACAAATTGCTTATGAATGCAGCTTTGGGTAGAAACTTGCTCATTTCTGTTATTTGTG
CCAGTCTAATGCACTGCCCAGTCATGTGAAGATCAGTGTGTCCTGGCAGACAGTGTTGGAAGATTCCTTCCAACAGATTA
TGGCATTAAAACCATATGACTTGAGGAGGAGATTATATGTAATATTAAGAGGAGAAGGACTTGATTATGGTGGTCTAGCA
AGAGAATAATTTTTCTTACTTTCACATGAAGTTTTGAACCCAATGTATTGTTTATTTGAGTATGCTGGCAAGAACAGCTA
CTCCCTGCAGATAAATCCGGCATCAACCATTAATCCAGATCATCTTTCATACTTTTGCTTCATTGGTTGCTTTATCACTG
TGGCACTTTTTTGTAGAAAGTTTATTGATACTGGTTTCTCTTTACCATTCTACAAGTGTTTGCTAAGTAAAAAATTTACT
GTTAAGGAATTGGAATCAATTGATACTGAATTTTATAACTCCCTTATCTGGATAAGAGACAATAATATTGAATAATGTGG
TTTAGAAATGTACTTTTCTGTTGACATGGAGATTCTGGGAAAGGTTACTTCACGTAACCTGAAATTGGGAGGTTCCAATA
TTCTGGTGACTGAAGAGAACAAAGATGAATATATTGGTTTAATGACAGAATGACATTTTTCTCAAGGAGTACAAGAACAG
ACCAAAGCTTTCCTTGATGGTTTTAATGAAGTTGTTCTCCTTCAATGGCTGCAGTACTTTGATGAAAAGGAATTAGAGGT
TATGTTGTGTGGCATGCAGGAGACTAACTTGGCAGATTGGCAGAGAAACACTGTTTATTGGCATTATACAAGAAACAGCA
AGCAAATAATTTGGTTTTGGCAGTTTGTGAAAGACAATGAAGTAAGAATGTGACTACTGCAGTTTGTCACTGGAACCTGC
TGTTTACCTCTAGGAGGGTTTGCTGAGCTCATGGGAAGTAATGGGTCTCAAAAATTTTGCATAGAAAAAGTTGGCAAAGA
CACCTGGTTACCAAGAAGTCACATGTGTTTTAATTGCTTGGATCTACCACCATATAAGAGTTATGAACAACTAAAGGAAA
AGCTTCTTTTTGCAATAGAAAGACAGAGGGATTTGGACAAGAA
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 |
Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_2100 was not experimentally validated.
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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000308 | 1 retrocopy | |
| Choloepus hoffmanni | ENSCHOG00000011115 | 1 retrocopy |
retro_chof_2100 ,
|
| Felis catus | ENSFCAG00000008780 | 1 retrocopy |