RetrogeneDB ID:

retro_dnov_34

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_9170:48776..49541(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000000193
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PGAM2
Ensembl ID:ENSDNOG00000024480
Aliases:None
Description:phosphoglycerate mutase 2 (muscle) [Source:HGNC Symbol;Acc:8889]


Retrocopy-Parental alignment summary:






>retro_dnov_34
ATGGCTGCCTACAAGTTGGTGCTGATCCGGCACGGCAAGAGCGCCTGGAACCTGGAGAACCGCTTCAGCGGTTGGTACGA
CGCCGACCTGAGCCCAGCGGGGCATGAGGAGGCGAAGCGCGGCGGGCAGGCGCTGCGAGATGCTGGCTATGAGTTTGACA
TCTGCTTCACCTCAGTGCAGAAGAGAGCAATCAGGACTCTGTGGACTGTGCTAGAAGCCATCGACCAGATGTGGCTGCCA
GTAGTGAGGACTTGGCGCCTCAATGAACGGCACTATGGGGGTCTGACTGGCCTCAATAAAGCAGAAACTGCTGCCAAGCA
TGGCGAAGCCCAAGTTAAAATCTGGAGGCGCTCCTATGATGTCTCACCACCACCGATGGAGCCAGATCATCCCTTCTACA
GCAACATCAGTAAGGATCGCAGGTATGCAGACCTCACTGAAGATCAGCTCCCCTCCTGTGAGAGTCTAAAGGACACTATT
GCCAGAGCCCTGCCTTTTTGGAATGAAGAAATTGTTCCCCAGATCAAGGAGGGGAAACGGGTATTGATTGCAGCACATGG
CAACAGTCTTCCGGGCATTGTCAAGCACCTGGAGGGTCTCACTGAAGAAGCTATCATGGAGCTGAACCTGCCCACTGGTA
TTCCCATTGTCTATGAGTTGGACAAGAACTTGAAGCCAATCAAACCTATGCAATTCCTAGGGGATGAAGAGACTGTACGG
AAGGCCATGGAAGCTGTGGCTGCCCAGGGCAAGGCTAAGAAGTAA

ORF - retro_dnov_34 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATHRLVIVRHGESTWNQENRFCGWFDAELSEKGAEEARRGAQAIKDAGMEFDICYTSVLKRAIRTLWTI
MA...LV..RHG.S.WN.ENRF.GW.DA.LS..G.EEA.RG.QA..DAG.EFDIC.TSV.KRAIRTLWT.
RetrocopyMAAYKLVLIRHGKSAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTV
ParentalLDGTDQMWLPVVRSWRLNERHYGGLTGLNKAETAAKHGEEQVKVWRRSFDVPPPPMDEKHPYYNAISKER
L...DQMWLPVVR.WRLNERHYGGLTGLNKAETAAKHGE.QVK.WRRS.DV.PPPM...HP.Y..ISK.R
RetrocopyLEAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVSPPPMEPDHPFYSNISKDR
ParentalRYAGLKAGELPACESLKDTIARALPFWNDEIAPQIKAGKRVLIAAHGNSLRGIVKHLENMSDQAIMELNL
RYA.L....LP.CESLKDTIARALPFWN.EI.PQIK.GKRVLIAAHGNSL.GIVKHLE.....AIMELNL
RetrocopyRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLPGIVKHLEGLTEEAIMELNL
ParentalPTGIPIVYELDEKLKPTKPMRFLGDEETVRKAMEAVAAQGKAK
PTGIPIVYELD..LKP.KPM.FLGDEETVRKAMEAVAAQGKAK
RetrocopyPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAK

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 85 .76 RPM 8 .36 RPM
SRP012922_cerebellum 89 .08 RPM 5 .64 RPM
SRP012922_heart 52 .44 RPM 2 .09 RPM
SRP012922_kidney 57 .22 RPM 3 .29 RPM
SRP012922_liver 31 .43 RPM 1 .39 RPM
SRP012922_lung 23 .06 RPM 2 .14 RPM
SRP012922_quadricep_muscle 10 .21 RPM 3583 .71 RPM
SRP012922_spleen 32 .28 RPM 2 .29 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_34 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 14 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000024480 1 retrocopy
retro_dnov_34 ,
Macropus eugenii ENSMEUG000000129208 retrocopies
Otolemur garnettii ENSOGAG000000067131 retrocopy
Procavia capensis ENSPCAG000000021811 retrocopy
Rattus norvegicus ENSRNOG000000135321 retrocopy
Tupaia belangeri ENSTBEG000000045871 retrocopy
Drosophila melanogaster FBgn00148691 retrocopy



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