RetrogeneDB ID:

retro_dnov_1575

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_238691:11..705(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSDNOG00000015893
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dnov_1575
CCCGAGCTGCAGGAGGCGCGGCCGCGCAGCCAGAGCACAGGCCGCAGGAGCTGCGGCGCCTCTGCCAGAACCCGCCACCG
CCGCGGCCCGGCTCCACAAAGCCCGAGCGTGTCACAGCCAGGACTTCCTCTCCAGGTCCCCTTCCAAAATGCAGCCACCG
CCGTCACCAGTCTCTGCAAAGAAAGCGTGGATACCCGTCAGCGAAGTTTTGATATTGGAATTCAGATTGGCTATCAGCGT
CGCAGTAAGGATGTGTTGGCTTGGGTTAAAAAACGCAGAAGAACTGTACGTAGAGAAGATTTGATCAGCTTCCTGTGTGG
AAAAGCTCCTCCACCTGGGAACTCTAGAGCTCCCCCAGGACTGACTGCAGTGCCCCCTAACGGAGCACTTCAGCGGAAGC
TAGCTCATCTGTAGAGGCTGGTTTGCAACCCTTCCGGGAAGCCGCGGCTCTGCACGGGCTTAGTGGTGCGATGGCCAGCA
TAGCGCGCTCCAGTCCCCAGGCTCTCCTCCACGGGTAAGCAGCGGATCGAATGCTCGTCGTCGGAGAAGTGGACTCCACG
ATGTCGATGTGAACACTTTCACATCAGAAGAAACGGCACTCCACTTGGACAATGGTGGAGCTAGAAAGCGTACCTCAGCC
CAATGGGGCGATGTCTTTACAGACTCAACAACCCATAAACGCAGCAGAATGATC

ORF - retro_dnov_1575 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.25 %
Parental protein coverage: 86.84 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalPELQEA-AAAQPEHKPRELRRLCQNP-ATAAARLHKDRVCQ-QPGLSLWVPFQNAATAVTNLYKESVDTH
PELQEA.AAAQPEH.P.ELRRLCQNP.ATAAARLHK.R.C..QPGL.L.VPFQNAATAVT.L.KESVDT.
RetrocopyPELQEA<AAAQPEHRPQELRRLCQNP<ATAAARLHKARACH<QPGLPLQVPFQNAATAVTSLCKESVDTR
ParentalQRSFDIGIQIGYQRRNKDVLAWV-KRRRTIRREDLISFLCGKAPPPRNSRAPPRLTVESPN-RATSTETS
QRSFDIGIQIGYQRR.KDVLAWV.KRRRT.RREDLISFLCGKAPPP.NSRAPP.LT...PN.R.TS.E.S
RetrocopyQRSFDIGIQIGYQRRSKDVLAWVKKRRRTVRREDLISFLCGKAPPPGNSRAPPGLTAVPPN<RSTSAEAS
ParentalSSVETDVQPFPETVALHGLSGAMASIARSSPGS-PPRVSSGSNARSRR-SGLHDVDVNTFTSEEMALHLD
SSVE...QPF.E..ALHGLSGAMASIARSSP....P...S......RR.SGLHDVDVNTFTSEE.ALHLD
RetrocopySSVEAGLQPFREAAALHGLSGAMASIARSSPQA<SPPRVSSGSNARRRRSGLHDVDVNTFTSEETALHLD
ParentalNGGARKRTSAQWGDVFTDSTTHKRNRMI
NGGARKRTSAQWGDVFTDSTTHKR.RMI
RetrocopyNGGARKRTSAQWGDVFTDSTTHKRSRMI

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 7 .78 RPM
SRP012922_cerebellum 0 .14 RPM 5 .36 RPM
SRP012922_heart 0 .00 RPM 5 .34 RPM
SRP012922_kidney 0 .55 RPM 3 .56 RPM
SRP012922_liver 0 .00 RPM 4 .64 RPM
SRP012922_lung 0 .15 RPM 10 .23 RPM
SRP012922_quadricep_muscle 0 .00 RPM 7 .27 RPM
SRP012922_spleen 0 .23 RPM 8 .70 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_1575 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 17 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000107192 retrocopies
Canis familiaris ENSCAFG000000189811 retrocopy
Cavia porcellus ENSCPOG000000109251 retrocopy
Dasypus novemcinctus ENSDNOG00000015893 3 retrocopies
retro_dnov_1575 , retro_dnov_2266, retro_dnov_827,
Equus caballus ENSECAG000000094301 retrocopy
Homo sapiens ENSG000001828311 retrocopy
Gorilla gorilla ENSGGOG000000107441 retrocopy
Monodelphis domestica ENSMODG000000053782 retrocopies
Mustela putorius furoENSMPUG000000147071 retrocopy
Mus musculus ENSMUSG000000225071 retrocopy
Nomascus leucogenys ENSNLEG000000101061 retrocopy
Otolemur garnettii ENSOGAG000000039091 retrocopy
Pongo abelii ENSPPYG000000070881 retrocopy
Pan troglodytes ENSPTRG000000077511 retrocopy
Rattus norvegicus ENSRNOG000000025452 retrocopies
Sus scrofa ENSSSCG000000284541 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000093241 retrocopy



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