RetrogeneDB ID:

retro_chof_466

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_112486:848..1670(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MTIF3
Ensembl ID:ENSCHOG00000004404
Aliases:None
Description:mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]


Retrocopy-Parental alignment summary:






>retro_chof_466
ATGGCTGCACTTTTTCTAAAGAAGTTAATCCTGCAAACTGTGAAGACTGAAATGAACTGCTTTGGAAGATGTTTTGGTAA
ACACGTGCAAAACACAGCACCAGCACCATTGTCCGTTATTGCTTCCGCCCCCAGACTCTTCTCCCTAACCCATGCAAAAT
TTTATAGTACTGTAGAAGAAAGCCAGGATGAAAGAAAAAAGAAAGTAAAAAGTGAAACAGCTTTTAGTAATACTGGAAGA
AAAATTAGTGAGCGAATTATTCGCATAATCGATGAGCACCGCAACGATTTAGGCAGCATGCACCGAGCAGACGTGATTAA
GCTCCTGGACGCGCGAGACCCGTGCTGTGAAAAGGAGCAGCAGCTCCGAGCCTCCAGAATACCGGCTCTTGAGGAGACTC
CTGTCCCCCGAAGAACTGCTCAGGCTCCGAGAAAGGGAAAAAGCCTTCCAAAACTGGACTGACACAGATAAAGGAATGGA
TTATTTTCTTCAATATGACAACATGATTTGGACACAAGAGTAAACAGATCAGAAATGGATTGACAAAAAATATCGAGTTC
AAATTACTGTAAAGAAAGGGAAGAGTGTAGAAGAGCCAGAAAATAAAGTGGAAGAGCTATTTAATCAGATCCTCCAGACC
ATGCTTGGAGTGGCCACCTTCTGAACCAGGCCACAAGCCATCAAAGGAGGAAAAGCTGCAATGTGTGTTCTTCCTCATTT
GAGCAAAAAAGGAGGAGGATGAGTACAGGGAAACTCAGGGGACCCAGAAAGGAGACAAAAGAAAATGTAAATGAAAATGA
TAGAAATTCAGTTGTTCTACAG

ORF - retro_chof_466 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.44 %
Parental protein coverage: 99.64 %
Number of stop codons detected: 2
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalMAALFLKRLILQTVKTETNCFGRCFGKHIVQKTAPAPLSIIASAPRLSFLTHAKFYSTVEDSQDERKKKQ
MAALFLK.LILQTVKTE.NCFGRCFGKH.VQ.TAPAPLS.IASAPRL..LTHAKFYSTVE.SQD......
RetrocopyMAALFLKKLILQTVKTEMNCFGRCFGKH-VQNTAPAPLSVIASAPRLFSLTHAKFYSTVEESQDXXXXXX
ParentalKTETAFSNTGRKISERIIRVIDEHGNDLGSMHRANVIKLLDARD-LRLVKRSSSSEPPEYQLMTGLQIHE
....AFSNTGRKISERIIR.IDEH.NDLGSMHRA.VIKLLDARD.......SSS.EPPEY.L...L...E
RetrocopyXXXXAFSNTGRKISERIIRIIDEHRNDLGSMHRADVIKLLDARD>RAVKRSSSS-EPPEYRLLRRLLSPE
ParentalERLRLREREKA-KPK-TGPTQIKEL-TFSSNIGQHDLDT-KSKQ-TQKWIEKKYRVQITIKKGKYVEEPE
E.LRLREREKA..PK.TG.TQIKE...FSS.I.QHDLDT.KSKQ..QKWI.KKYRVQIT.KKGK.VEEPE
RetrocopyELLRLREREKA<LPK<TGLTQIKEW>LFSS-I*QHDLDT<KSKQ<DQKWIDKKYRVQITVKKGKSVEEPE
ParentalNKMEELFNQILQTMPGMATFSTRPQAIKGGKATMCVLRHLS-KKEEDEYRETQGTQKGDLTK-ENGNEKE
NK.EELFNQILQTM.G.ATF.TRPQAIKGGKA.MCVL.HLS.KKEEDEYRETQGTQKGD..K..N.N...
RetrocopyNKVEELFNQILQTMLGVATF*TRPQAIKGGKAAMCVLPHLS>KKEEDEYRETQGTQKGDKRK>VNENDRN
ParentalLSCLQ
...LQ
RetrocopySVVLQ

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_466 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 8 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000004404 1 retrocopy
retro_chof_466 ,
Homo sapiens ENSG000001220331 retrocopy
Gorilla gorilla ENSGGOG000000084091 retrocopy
Nomascus leucogenys ENSNLEG000000003431 retrocopy
Oryctolagus cuniculus ENSOCUG000000117211 retrocopy
Pongo abelii ENSPPYG000000052361 retrocopy
Pan troglodytes ENSPTRG000000057321 retrocopy
Tupaia belangeri ENSTBEG000000122763 retrocopies



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