RetrogeneDB ID:

retro_dnov_2252

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_58828:9777..10505(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GABRG1
Ensembl ID:ENSDNOG00000003474
Aliases:None
Description:gamma-aminobutyric acid (GABA) A receptor, gamma 1 [Source:HGNC Symbol;Acc:4086]


Retrocopy-Parental alignment summary:






>retro_dnov_2252
GATGTCACTCTCATTCTCAACAAGTTGCTAAGAGAGTATGACAAAAAGCTGAGGCCAGATATTGGAATATAACCGACCGT
AATTGATGCTGACATTGATTCAAACAGTATTGGGCCTGTGTCATCAATAAACATGGAATACCAAACTGATATCTTTTTCG
CTCAGACCTGGACAGACAGCCGCCTTCGATTCAACAGCACAATGAAAATACTTAACTCTGAATAGCAACATGGTTGGATT
AATATGAATTCCAGAATAATCTTTCGCAATTCCAAAACTGCAGAGGCTCACGGGATTACTACACCCAATCAACGCCTCAG
AATTTGGAATGCTGGGAAAATCCTTTCTACTTCAAGGCTCACCATAAACGTGGAGTGCCAGCTGCAGCTGCACAGCTTCC
CCACGGATGAGCACTCGTGCCCACTGACTTTCTCCAGCTATGGCTACCCCAAAGAAGACATGATTTATAGACGGAGAAAA
AATTCAGTGGCGGCAGCTGATCAGAAATCGTGGCGGCTTTATCAGTTTGACTTCATGGGTCTCAGAAACACCACCGAAAC
TGTGACAACATCTGCAGGTGATTATGTTGTCATGACTATATATTTTGAATTAAGTAGAAGAATGGGATACTTCACTATTC
AGACGTACATCCCGGTATACTTACTGTGGTTTTATCTTGGGTGTCGTTTTGGATCAAAAAAGACGCTACACCAGCGAGAA
CAGCATTA

ORF - retro_dnov_2252 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.92 %
Parental protein coverage: 58.84 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDITQILNSLLQGYDNKLRPDIGVRPTVIETDVYVNSIGPVDPINMEYTIDIIFAQTWFDSRLKFNSTMKV
D.T.ILN.LL..YD.KLRPDIG..PTVI..D...NSIGPV..INMEY..DI.FAQTW.DSRL.FNSTMK.
RetrocopyDVTLILNKLLREYDKKLRPDIGI*PTVIDADIDSNSIGPVSSINMEYQTDIFFAQTWTDSRLRFNSTMKI
Parental-LMLNSNMVGKIWIPD-TFFRNSRKSDAHWITTPNRLLRIWNDGRVLYTLRLTINAECYLQLHNFPMDEH
.L.LNSNMVG.I.IP....FRNS....AH.ITTPN..LRIWN.G..L.T.RLTIN.EC.LQLH.FP.DEH
Retrocopy>LTLNSNMVGLI*IPE<IIFRNSKTAEAHGITTPNQRLRIWNAGKILSTSRLTINVECQLQLHSFPTDEH
ParentalSCPLEFSSYGYPKNEIEYKWKKPSVEVADPKYWRLYQFAFVGLRNSTEISHTISGDYIVMTIFFDLSRRM
SCPL.FSSYGYPK....Y...K.SV..AD.K.WRLYQF.F.GLRN.TE...T..GDY.VMTI.F.LSRRM
RetrocopySCPLTFSSYGYPKEDMIYRRRKNSVAAADQKSWRLYQFDFMGLRNTTETVTTSAGDYVVMTIYFELSRRM
ParentalGYFTIQTYIPC-ILTVVLSWVSFWINKDAVPARTSL
GYFTIQTYIP..ILTVVLSWVSFWI.KDA.PART.L
RetrocopyGYFTIQTYIPV<ILTVVLSWVSFWIKKDATPARTAL

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






RNA-Seq - click to see more details

(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 .00 RPM
SRP012922_cerebellum 0 .00 RPM 1 .92 RPM
SRP012922_heart 0 .00 RPM 0 .00 RPM
SRP012922_kidney 0 .00 RPM 0 .00 RPM
SRP012922_liver 0 .00 RPM 0 .00 RPM
SRP012922_lung 0 .00 RPM 0 .00 RPM
SRP012922_quadricep_muscle 0 .00 RPM 0 .00 RPM
SRP012922_spleen 0 .00 RPM 0 .23 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_2252 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000003474 1 retrocopy
retro_dnov_2252 ,


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