RetrogeneDB ID:

retro_dnov_2405

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_72059:1553..1957(+)
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:ENSDNOG00000018545
Aliases:None
Description:thiamin pyrophosphokinase 1 [Source:HGNC Symbol;Acc:17358]


Retrocopy-Parental alignment summary:






>retro_dnov_2405
TTTTTGCCTAAATACATCAAGGCAGATTTTGATTCCATTAGGCCTGAAGTCAATGGGTACTATACTTGTAAATGATGTGA
GCTGATTTCAACTCCTGATCAAAACTGCACTGACTTTACCAATTACCTTCTAGTACTCTAAAAGAAGATAGATGTAAAAC
ACCTACAGGTTAATATGAATGTCACACTCCCAGGACTTGCTGGACATTTTGAATGGAGTATGGCATCTGTGTGTACCCTA
TTTCAAGTGAATCATATAACTCTTTGCCAATTATAATAATTCAAGAGGAAACTCTCATCTACCTGCCCCAACCAGGAAAG
GAAAAGATTCATGTAAACACTGGAATAGAAGATGATTGTTGTGGCCTTATTCCTGTTGTATGATAACACAATCACATTGC
CACA

ORF - retro_dnov_2405 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.71 %
Parental protein coverage: 55. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFLPEFINGDFDSIRPEVKEYYTSKGCELISTPDQNYTDFTKCLLELQKKIEEKNLEIDMIVTLGGLAGHF
FLP..I..DFDSIRPEV..YYT.K.CELISTPDQN.TDFT..LL.L.KKI..K.L...M.VTL.GLAGHF
RetrocopyFLPKYIKADFDSIRPEVNGYYTCK*CELISTPDQNCTDFTNYLLVL*KKIDVKHLQVNMNVTLPGLAGHF
ParentalDQIMS---ILFQATHIT-PLPLIIIQEESLIYLPQPGKHKLHVNTGMEGDWCGLVPIGQHCNHVTT
...M.....LFQ..HIT..LP.IIIQEE.LIYLPQPGK.K.HVNTG.E.D.CGL.P.....NH..T
RetrocopyEWSMASVCTLFQVNHIT<SLPIIIIQEETLIYLPQPGKEKIHVNTGIEDDCCGLIPVV**HNHIAT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 0 .00 RPM 0 .39 RPM
SRP012922_cerebellum 0 .00 RPM 0 .27 RPM
SRP012922_heart 0 .00 RPM 0 .23 RPM
SRP012922_kidney 0 .00 RPM 1 .37 RPM
SRP012922_liver 0 .00 RPM 1 .08 RPM
SRP012922_lung 0 .00 RPM 1 .37 RPM
SRP012922_quadricep_muscle 0 .00 RPM 0 .35 RPM
SRP012922_spleen 0 .00 RPM 0 .69 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_2405 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 ENSCHOG0000000122723 retrocopies
Dasypus novemcinctus ENSDNOG00000018545 4 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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