RetrogeneDB ID:

retro_dnov_945

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_125580:4560..4779(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SVIP
Ensembl ID:ENSDNOG00000016735
Aliases:None
Description:small VCP/p97-interacting protein [Source:HGNC Symbol;Acc:25238]


Retrocopy-Parental alignment summary:






>retro_dnov_945
ATGGGGCTGTGTTTTCCTTGCCCCGGGGAGGCTGAGCCTCCCTCAGCGGACCCAGAAGAGAAAAGAACAAAACTTGCAGA
AGCTACTGAGAGAAGACAGAGGTAGGCTGCATCTCGGGGCATTTTGGATGTTCAATCTGTGGAAGAAAAGAGGAAGAAAA
AGGAAAGATTAGAAAAACAAATCACTACAACTGGACCCCCACCAGAAGGTGGACTTAGA

ORF - retro_dnov_945 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.6 %
Parental protein coverage: 96.05 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGLCFPCPGEAEPPSPDPEEKRAKLAEAAERRQREAASRGILNVQSVEEKRKKKERLEKQITTTGPPPEG
MGLCFPCPGEAEPPS.DPEEKR.KLAEA.ERRQR.AASRGIL.VQS...............TTTGPPPEG
RetrocopyMGLCFPCPGEAEPPSADPEEKRTKLAEATERRQR*AASRGILDVQSXXXXXXXXXXXXXXXTTTGPPPEG
ParentalGLR
GLR
RetrocopyGLR

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 2 .53 RPM
SRP012922_cerebellum 0 .00 RPM 9 .62 RPM
SRP012922_heart 0 .00 RPM 6 .03 RPM
SRP012922_kidney 0 .00 RPM 5 .75 RPM
SRP012922_liver 0 .00 RPM 2 .63 RPM
SRP012922_lung 0 .00 RPM 7 .64 RPM
SRP012922_quadricep_muscle 0 .00 RPM 9 .87 RPM
SRP012922_spleen 0 .00 RPM 7 .10 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_945 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 3 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000131524 retrocopies
Dasypus novemcinctus ENSDNOG00000016735 4 retrocopies
Sus scrofa ENSSSCG000000228381 retrocopy



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