RetrogeneDB ID:

retro_chof_468

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_112618:71..784(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPK1
Ensembl ID:ENSCHOG00000001227
Aliases:None
Description:thiamin pyrophosphokinase 1 [Source:HGNC Symbol;Acc:17358]


Retrocopy-Parental alignment summary:






>retro_chof_468
ATGGAGCATATCTTTACCCTCTTGGAACGCCTGCTTTCCACTGGAATTTTAAGTATTGCTTTCTGATTCTGAACCAGCCT
TGGGACGACTGTTTTGGTCATCTTTGGAACACAGCTCTTTTAAAAGCCTGTGCTGATAGAGGTGCCAACTGCTTATATGA
TATCACCTAAGGAGAGTGGGAAAGCTCTTTGCCTGAATTCATCAATGGAGATTTTGATTCTATTAGGTCTGAAGTTAGAC
AGTAATACAGTATTAAGGGTCATGAGCTGATTTCAATTCCCAGTCAAGACCATAATGACTTTACCAAGTACCTCCAAGTG
CTCCAAAGGAAGACAGAAGAAAAAGCCCTACAGGTTGATACAGTTCTGACACTGGGAGGACTTGGTGGATTTTTTGACCA
GATTATGGCTTCTGTGAGCTCCCTCTTTCAAGTGACTGATGTCATTCCTTTGCCAATTATAATAATTTAAGAGAAGTCTC
TCATCTACCTGCTGCAATCAGGAAAGCACAAGTTGCATGTAAACACTGGAATGGAAAATGACTGGTGTGGCCTCATACCT
GTTGGACAGCCTCACAATCAGGTTACCATGTGGAACCTCACCAACTATATGTTTGATTTTGGAGTACTGGTCAGTACTTC
CAATACCTACAAAGGATCTGGAGTAGTGACTGTGGAAACTGAGCAGCTGCTCCTCTACACCATGGGCATCAAA

ORF - retro_chof_468 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.47 %
Parental protein coverage: 99.59 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEHVFTPLELLLPSG-NLKYCLLILNQPLDDCFRHLWSKALLKACADGGANRLYDITEGERESILPELIN
MEH.FT.LE.LL..G.N.KYC.LILNQP.DDCF.HLW..ALLKACAD.GAN.LYDIT.GE.ES.LPE.IN
RetrocopyMEHIFTLLERLLSTG<NFKYCFLILNQPWDDCFGHLWNTALLKACADRGANCLYDIT*GEWESSLPEFIN
ParentalGDFDSIRTEVRKHYSIKGCELISTPDQDNTDFTKCLQVLQKKIEEKALQVDMIVTLGGLGGRFDQIMASV
GDFDSIR.EVR..YSIKG.ELIS.P.QD..DFTK.LQVLQ.K.EEKALQVD...TLGGLGG.FDQIMASV
RetrocopyGDFDSIRSEVRQ*YSIKGHELISIPSQDHNDFTKYLQVLQRKTEEKALQVDTVLTLGGLGGFFDQIMASV
ParentalNTLFQAIDITPLPIIIIQDKSLIYLLQPGKHKLHVNTGMEGDWCGLIPVGQPCNHVTTTGLKWNLXNHVL
..LFQ..D..PLPIIII..KSLIYLLQ.GKHKLHVNTGME.DWCGLIPVGQP.N.VT.....WNL.N...
RetrocopySSLFQVTDVIPLPIIII*EKSLIYLLQSGKHKLHVNTGMENDWCGLIPVGQPHNQVT----MWNLTNYMF
ParentalGFGILVSTFNTYTYDGSGVVTVDTDQPLLWTMAIK
.FG.LVST.N..TY.GSGVVTV.T.Q.LL.TM.IK
RetrocopyDFGVLVSTSN--TYKGSGVVTVETEQLLLYTMGIK

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_468 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 7 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000001227 23 retrocopies
Dasypus novemcinctus ENSDNOG000000185454 retrocopies
Macropus eugenii ENSMEUG000000100621 retrocopy
Myotis lucifugus ENSMLUG000000042131 retrocopy
Monodelphis domestica ENSMODG000000254682 retrocopies
Ornithorhynchus anatinus ENSOANG000000207281 retrocopy
Vicugna pacos ENSVPAG000000102142 retrocopies



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