RetrogeneDB ID:

retro_dnov_2577

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_87042:41390..42067(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAD51C
Ensembl ID:ENSDNOG00000004696
Aliases:None
Description:RAD51 paralog C [Source:HGNC Symbol;Acc:9820]


Retrocopy-Parental alignment summary:






>retro_dnov_2577
TCCTGTGTTGAAATGCAGCGAATTTAGGGAGTTTCCGGCTGTCCAAAGTGGCACGGGTGAAATTAGTCTCTGCGGGTTTC
CAGACTGCTGAGGAGCTCCTGGTGGTGAAAGCTTAAGAGCTCAGAAAAGAAATTGGGATATCTAAAGAGGAAGATTTAGA
AACTCTACATATTATAAGAAGAGAATGTCTCTTAAATATACCAATGCATGCTGGTACATCTGAGACAGGCAAAAATAAAT
GTACAGCAGTGGAACTTCTTGAGCACGAGCATACCCAGGGCTTCATAATTACCTTTTGCTCAGCACTAGATAATATTCTT
GGGGGTGAAGTACCCTTAACCAAAACAACAGAAATCTGTGGTTCACCTGGTGTTGGAAAAACACAATTATGTATGCAATT
GGCAGTAGATGTGCCGATACCATAATGTTTTGGAGGAGTGACAGGGGAAACAGTTTTTATTGATACAGAGGGAAGTTTTA
TGGTGGACGGAGTTGTAGCCCTTGCCACTGCCTGAATTCAGTGTCTTCATCTTATAGCACGAACACACATGGGAGAGGAG
CACCAAAAGGCTTTGGAAGATTTCACTCTTGAAAATATTCTTTCCCATATTTATTATTTTCGTTGTCATGATTACATACA
TAGAACTCTTAGCACAAATTTATCTCCTTCCAGACTT

ORF - retro_dnov_2577 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.5 %
Parental protein coverage: 60.48 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSCVEMQR-DLGSFPLSTAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKEEALETLHIIRRECLLNIPR
SCVEMQR..LGSF.LS...RVKLVSAGFQTAEELL.VK..EL.KE.GISKEE.LETLHIIRRECLLNIP.
RetrocopySCVEMQR<NLGSFRLSKVARVKLVSAGFQTAEELLVVKA*ELRKEIGISKEEDLETLHIIRRECLLNIPM
ParentalHANTSETGK-KCTALELLEQEHTQGFIITFCSALDNILGGGVPLTKTTEICGAPGVGKTQLCMQLAADEQ
HA.TSETGK.KCTA.ELLE.EHTQGFIITFCSALDNILGG.VPLTKTTEICG.PGVGKTQLCMQLA.D..
RetrocopyHAGTSETGKNKCTAVELLEHEHTQGFIITFCSALDNILGGEVPLTKTTEICGSPGVGKTQLCMQLAVDVP
ParentalIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLHLIAGTHMGEKHQKALEDFTLENILSHIYYFRC
IP.CFGGV.GE.VFIDTEGSFMVD.VV.LATA.IQ.LHLIA.THMGE.HQKALEDFTLENILSHIYYFRC
RetrocopyIP*CFGGVTGETVFIDTEGSFMVDGVVALATA*IQCLHLIARTHMGEEHQKALEDFTLENILSHIYYFRC
ParentalHDYTELLAQIYLLPDFL
HDY........L.P..L
RetrocopyHDYIHRTLSTNLSPSRL

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 6 .22 RPM
SRP012922_cerebellum 0 .14 RPM 9 .21 RPM
SRP012922_heart 0 .23 RPM 3 .71 RPM
SRP012922_kidney 0 .00 RPM 7 .39 RPM
SRP012922_liver 0 .00 RPM 3 .10 RPM
SRP012922_lung 0 .15 RPM 9 .01 RPM
SRP012922_quadricep_muscle 0 .17 RPM 1 .38 RPM
SRP012922_spleen 0 .69 RPM 22 .32 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_2577 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 3 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000004696 3 retrocopies
retro_dnov_239, retro_dnov_2577 , retro_dnov_946,



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