RetrogeneDB ID:

retro_dnov_1511

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_22090:41181..42027(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSDNOG00000013620
Aliases:None
Description:lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]


Retrocopy-Parental alignment summary:






>retro_dnov_1511
CTGGCAGATGAACTGGTTCTTGTGGATGTCATAGAAGACAAATTGAAGGGAGAGATGATGATCTCCAACCTGGCACCCTT
TTCCTTAGAACACCAACCATTGTCTCTGGCAAAGACTATAGTGTGACTGCAAACTTCAAGTTGGTTATTATCACAGCTGG
GGCACATCAGCAAGAGGGAGAAAGCCATTTTAATTTGGTCCAGCATAACGTAAACATCTTTAAACTCATCATTGCTAATA
TTGTAAAATACAGCCCGAACTGCAAGTTGCTTGTTGTTTCCAATCCAGTGGATATCTTGACCTTTGTGGCTTGGAAACAA
GTGGCTTTCCCAAAAACCATGTTATTGGAAGTGATTGCAATCTGGATTCAGCCTGGTTCCCTTACCTAATGGAGGAGAGG
CTGGAGGTTCACCCATTAAGCTGTCATGGATGGGTCCTTGGGGAACATTGAGACTCTGGTGTGCCTGTGTGGAGTGGCGT
GAATGGTGCTGGTGTTTCCTTGAAAAAGCTGCAGCCTGATTGAGACACTGAAGCAGATAAGTAACAGTGGAAAGAGGTTC
ACAAACAGGTGGTTGACAGTGCTTATGAGGTGCTCAAACTGAAAGGCTATACTTCATGGGTCATTGGACTGTCTGTGGCA
GATTTGACAGAAACTCTAATCAAGAATCTTAGATGTGTACATCCAATTTCTACCATGATTAAGGAAGTCTATGGAATAAA
AGGTGATGTCTTTCTTAGAGTTCCTTGCATCTTGGACAGAATGGAATCTTAGATGTTGCCAAGGTGTTACTGCCTGCTGA
AGAAGAGACCCATTTGAAGAAGAGTGCAGATACACTTTGGGGGATC

ORF - retro_dnov_1511 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.43 %
Parental protein coverage: 97.25 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLTDELALVDVLEDKLKGEMM-DLQHGSLFLQTPKIVADKDYSVTANSKVVVVTAGVRQQEGESRLNLVQR
L.DEL.LVDV.EDKLKGEMM.DLQ.G.LFL.TP.IV..KDYSVTAN.K.V..TAG..QQEGES..NLVQ.
RetrocopyLADELVLVDVIEDKLKGEMM<DLQPGTLFLRTPTIVSGKDYSVTANFKLVIITAGAHQQEGESHFNLVQH
ParentalNVNVFKFIIPQIIKYSPDCIIIVVSNPVDILTYVTWK-LSGLPKHRVFGSGCNLDSARFRYLMAEKLGVH
NVN.FK.II..I.KYSP.C...VVSNPVDILT.V.WK..SG.PK..V.GS.CNLDSA.F.YLM.E.L.VH
RetrocopyNVNIFKLIIANIVKYSPNCKLLVVSNPVDILTFVAWK<TSGFPKNHVIGSDCNLDSAWFPYLMEERLEVH
ParentalPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPDMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWA
P.SCHGW.LGEH.DS.V.VWSGVN.AGVSL..L.PD..T..D...WKEVHK.VV.SAYEV.KLKGYT.W.
RetrocopyPLSCHGWVLGEH*DSGVPVWSGVNGAGVSLKKLQPD*DTEADK*QWKEVHKQVVDSAYEVLKLKGYTSWV
ParentalIGLSVADLIESLFKNLSRIHPVSTMVKGMYGIENEVFLSLPCILN-ARGLTSVINQKLKDDEVAQLKKSA
IGLSVADL.E.L.KNL...HP.STM.K..YGI...VFL..PCIL....G...V....L...E...LKKSA
RetrocopyIGLSVADLTETLIKNLRCVHPISTMIKEVYGIKGDVFLRVPCILD<QNGILDVAKVLLPAEEETHLKKSA
ParentalDTLWDI
DTLW.I
RetrocopyDTLWGI

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 299 .29 RPM
SRP012922_cerebellum 0 .00 RPM 408 .56 RPM
SRP012922_heart 0 .00 RPM 1695 .69 RPM
SRP012922_kidney 0 .00 RPM 900 .24 RPM
SRP012922_liver 0 .00 RPM 13 .47 RPM
SRP012922_lung 0 .00 RPM 184 .19 RPM
SRP012922_quadricep_muscle 0 .00 RPM 987 .97 RPM
SRP012922_spleen 0 .00 RPM 156 .93 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_1511 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 19 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
Canis familiaris ENSCAFG000000121959 retrocopies
Cavia porcellus ENSCPOG000000071381 retrocopy
Dasypus novemcinctus ENSDNOG00000013620 4 retrocopies
Dasypus novemcinctus ENSDNOG0000001891511 retrocopies
Felis catus ENSFCAG000000126391 retrocopy
Gorilla gorilla ENSGGOG000000157581 retrocopy
Loxodonta africana ENSLAFG000000009722 retrocopies
Macropus eugenii ENSMEUG000000048251 retrocopy
Microcebus murinus ENSMICG000000171832 retrocopies
Myotis lucifugus ENSMLUG000000121551 retrocopy
Macaca mulatta ENSMMUG000000026794 retrocopies
Monodelphis domestica ENSMODG000000177861 retrocopy
Mustela putorius furoENSMPUG000000001725 retrocopies
Mus musculus ENSMUSG000000302464 retrocopies
Otolemur garnettii ENSOGAG000000047639 retrocopies
Pteropus vampyrus ENSPVAG000000024623 retrocopies
Rattus norvegicus ENSRNOG000000130003 retrocopies
Sus scrofa ENSSSCG000000005761 retrocopy



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