RetrogeneDB ID:

retro_dnov_239

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_2907:112122..112766(+)
Located in intron of:ENSDNOG00000000503
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_239
AAGGGAAGTTTTATGGTAGACCTTGCTAGCCACCTGCATTCAGCATCTTCATCCCATAACAGGGAACACACATGGGAGAG
GGAGCACCAAAAACCTTTGGAGTTCACTCTTGAAAATATTCTTTCCCATATTTATTATTTTCATTGTCATGATTATACAG
AACTTTTGGCACAAATTTGTCTCCTTCTAGACTTCCTTTCAGAGCTTTCACTCAAAGCTTCCATTAGTGATAGTGGATGG
CTTTGCTTTTCCTTTTCATCATGACCTAGATGACCTTTCACTTTGTACTCAGTTACTGATTGGCCTAACCCAGCAAATGA
TCAGTTTTGTAAATAACCACAGATTGGCTGTAATTTTAACCAATCAGATGACAACAAAGTTGGATAGAAATAAGGTCTCA
CTGTTCTTGCTTTAGGGGGAAGTTGAGGACATGCTGCTACAATACAGTTTATCTTTCACTGGAACAGAAAGCAGAGGTTG
GCAACACTGTATAAATCACCAAGCCAGAAGGAATCCACAATATTGCATCACATCTCAGGGATTTAGATGTTGCTAAACAT
TTTGCTGCTACTACATGTTTATAGCCAATAGAAGCTTCCTTGAATTCCTGGAAATGGTCACAAGACTCAGAAGAAGAACA
GAAA

ORF - retro_dnov_239 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.44 %
Parental protein coverage: 58.33 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalEGSFMVDRVVDLAT-ACIQHLHLIAG-THMGE-KHQKALEDFTLENILSHIYYFRCHDYTELLAQIYLLP
.GSFM....VDLA...CIQHLH.I.G.THMGE..HQK.LE.FTLENILSHIYYF.CHDYTELLAQI.LL.
RetrocopyKGSFM----VDLAS>TCIQHLHPITG>THMGE>EHQKPLE-FTLENILSHIYYFHCHDYTELLAQICLLL
ParentalDFLSEHSKVRLVIVDG-IAFPF-RHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKFDKNQT
DFLSE.S........G...F.F..HDLDDLSL.T.LL.GL.QQMIS..NNHRLAVILTNQMTTK.D.N..
RetrocopyDFLSELSLKASISDSGWLCFSF>HHDLDDLSLCTQLLIGLTQQMISFVNNHRLAVILTNQMTTKLDRNKV
ParentalSL-VPALGESWGHAATIRLIFHWDRKQRLATLCKSPNQKESTVLFQIT-QGFRVAKHFAATTCL-PIEAS
SL.V.ALG.S.GHAATI..IFHW.RKQRLATL.KSP.QKEST.L..I......VAKHFAATTCL.PIEAS
RetrocopySL<VLALGGS*GHAATIQFIFHWNRKQRLATLYKSPSQKESTILHHIS<RDLDVAKHFAATTCL*PIEAS
ParentalLNSWKWSQDSEEEQK
LNSWKWSQDSEEEQK
RetrocopyLNSWKWSQDSEEEQK

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 6 .22 RPM
SRP012922_cerebellum 0 .00 RPM 9 .21 RPM
SRP012922_heart 0 .00 RPM 3 .71 RPM
SRP012922_kidney 0 .00 RPM 7 .39 RPM
SRP012922_liver 0 .15 RPM 3 .10 RPM
SRP012922_lung 0 .00 RPM 9 .01 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .38 RPM
SRP012922_spleen 0 .00 RPM 22 .32 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_239 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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