RetrogeneDB ID:

retro_dnov_508

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_5501:12191..13061(-)
Located in intron of:ENSDNOG00000019660
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GNPDA1
Ensembl ID:ENSDNOG00000007804
Aliases:None
Description:glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]


Retrocopy-Parental alignment summary:






>retro_dnov_508
ATAAGGCTTATCATCCTCCACCACTATTCTCAGGCCAATGAGTGGCAGCCAAGTACACCAGGAACCGCATCATCCAGTTT
AACCTAGGGCCAGAGAAGTACTTCACTCTGGGGCTTCCCACTGGGAGCACCCCACTTGGCTGCTACAAGAAGCTGATTGA
ATACTGTAAGAACGGGGACTTGTCCTTCAAATACATAAAGACCTTCAACATGGACGACGTATGTGGGCCTTCCTCGAGAC
CACCCAGGGAGTTACCACTCCTTCACGTGGAACAACTTCTTCAAGCACATTGACTTCCATCCAGAAAACACCCATATCCT
GGATGGGAATGCAGCTGACTTGCAGGCTGAGGGTGATGATGCCTTTGAAGAGAAGATCACAGCTGCAGGTGGGATTGAGC
TGTTTGTTGGAGGCATTGGCCCCGACAGACATATCGCCTTCAACGAGCCGGGCTCCAGTCTGGGGTCCAGGACCCGTGTG
AAGACACTGGCCATGGACACCATCCTGGCCAACGCCAGGTTCTTCAATGGGGAGCTCACCAAGGTGCCCGCCATGGCCCT
GACGGTGGGCGTGGGCACCATCACGGATGCTCGGGAGGTGATGATCCTCATCACGGGGGCGCACGAGGCGTTTGCTCTGT
ACAAGGCCATCGAGGAGGGAGTGAGCCACATGTGGACTGGGTCTGCCTTCCAGCAGCATCCCCGCACAGTGTTCGTGTGT
GACGAGGATGCCACCCTAGAGCTCAAAGTGAAGACTGTCAAGTATTTCAAAGGTTTAATGCTTGTTCATGACAAGTTGGT
GGACCCCTTGTACAGTATCAAAGAGAAGGAAACAGAGAAAAGCCAATCTTCCAAGACACCATACAGCGAT

ORF - retro_dnov_508 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.38 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMKLIILDDYSQASEW-AAKYIRNRIIQFNPGPDKYFTLGLPTGSTPLGCYKKLIEYYKNGDLSFKYVKTF
..LIIL..YSQA.EW.AAKY.RNRIIQFN.GP.KYFTLGLPTGSTPLGCYKKLIEY.KNGDLSFKY.KTF
RetrocopyIRLIILHHYSQANEW<AAKYTRNRIIQFNLGPEKYFTLGLPTGSTPLGCYKKLIEYCKNGDLSFKYIKTF
ParentalNMDE-YVGLPRDHPESYHSFMWNNFFKHIDIHPGNTYILDGNAADLQAECE-SFEEKITAAGGIELFVGG
NMD..YVGLPRDHP.SYHSF.WNNFFKHID.HP.NT.ILDGNAADLQAE....FEEKITAAGGIELFVGG
RetrocopyNMDD>YVGLPRDHPGSYHSFTWNNFFKHIDFHPENTHILDGNAADLQAEGDDAFEEKITAAGGIELFVGG
ParentalIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFNGELARVPTMALTVGVGTIMDAREVMILITGAH
IGPD.HIAFNEPGSSL.SRTRVKTLAMDTILANARFFNGEL..VP.MALTVGVGTI.DAREVMILITGAH
RetrocopyIGPDRHIAFNEPGSSLGSRTRVKTLAMDTILANARFFNGELTKVPAMALTVGVGTITDAREVMILITGAH
ParentalKAFALYKAIEEGVSHMWTVSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHNKLVDPLYSIKEKET
.AFALYKAIEEGVSHMWT.SAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVH.KLVDPLYSIKEKET
RetrocopyEAFALYKAIEEGVSHMWTGSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHDKLVDPLYSIKEKET
ParentalEKSQSSKTPYSD
EKSQSSKTPYSD
RetrocopyEKSQSSKTPYSD

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 .19 RPM 27 .42 RPM
SRP012922_cerebellum 0 .27 RPM 3 .85 RPM
SRP012922_heart 0 .23 RPM 2 .09 RPM
SRP012922_kidney 0 .55 RPM 24 .09 RPM
SRP012922_liver 0 .62 RPM 13 .00 RPM
SRP012922_lung 1 .07 RPM 5 .80 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .56 RPM
SRP012922_spleen 0 .92 RPM 18 .66 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_508 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 9 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000078651 retrocopy
Choloepus hoffmanni ENSCHOG000000098842 retrocopies
Dasypus novemcinctus ENSDNOG00000007804 3 retrocopies
retro_dnov_1363, retro_dnov_1608, retro_dnov_508 ,
Macropus eugenii ENSMEUG000000154421 retrocopy
Monodelphis domestica ENSMODG000000103981 retrocopy
Mus musculus ENSMUSG000000521021 retrocopy
Otolemur garnettii ENSOGAG000000073033 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000165081 retrocopy
Tupaia belangeri ENSTBEG000000033302 retrocopies



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