RetrogeneDB ID:

retro_dnov_2085

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_465:103258..103958(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LIX1
Ensembl ID:ENSDNOG00000012335
Aliases:None
Description:Lix1 homolog (chicken) [Source:HGNC Symbol;Acc:18581]


Retrocopy-Parental alignment summary:






>retro_dnov_2085
GTGAGTGTGGTGGAGGCGCTGCAGCAGTTCTGGCAGATGAAGCAGTCCCTTGGGGCTGACTTGAAGAATGGGGCTTTAGC
GGTTTTGAGATGGTGCCTACCAACAGCCCTCTCTATGTCTGCTATGTCACCCTGCCGGGGGGAAGTTGCTTTGGGAGTTT
CCAGGTTTGTCCCACAAAAGCTGAGGCTCGGCGGAGTGCTGCAAAGATTGCACTAATGAACTCTGTGTTTAATGCACATC
CTTCCCGGAGAATCACTGATGAGTTCATTGAGAAGAGTGTCTCTGAGCCTTTGGCATCTTTCAGCGGCAACAGGGAGGAG
GCTGACAACCCAAATACAGGGACTGGTGCCTTCGGATTCATGTTGGAACCCAACAAGGGCAAGTCAGTGTTGGAGTTCCA
GGAGTTAATGACAGTTTTTCAACTGCTGCACTGGAATGGCAGCCTTCAGGCCATGAGGGAAAGACCGAGCTCTCAGCAAG
AGGTGCTGGCTCATTATTCACCCCCAGCCCTGGATGATGATATTCGCCACCAAATGGCATTGCACTGGGTGAGCCGGGAG
AGAGTGTGCCAGGGGCACTGTCTAGAGAGCTGGCCTCCACTGAGTGGGAGCTGGATGAAGCCTGGCTGGGAGGCAAGTTG
CTGTGCTTCCACAAGGAGAAGAAAGATATTCTCATGCTGGCTGCTGGGCAGTTGGGCAAC

ORF - retro_dnov_2085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.27 %
Parental protein coverage: 82.92 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLNVVSMLQEFWESKQQQRAAFPSEGIVV-YESLPSPGPPFVSYVTLPGGSCFGNFQCCLSRAEARRDAAK
..VV..LQ.FW..KQ...A........V..E..P...P..V.YVTLPGGSCFG.FQ.C...AEARR.AAK
RetrocopyVSVVEALQQFWQMKQSLGADLKNGALAV<FEMVPTNSPLYVCYVTLPGGSCFGSFQVCPTKAEARRSAAK
ParentalVALINSLFNELPSRRITKEFIMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTMLEFQELMTI
.AL.NS.FN..PSRRIT.EFI..SV.E..AS.SG....AD.P.T..GA...MLE.N.GK..LEFQELMT.
RetrocopyIALMNSVFNAHPSRRITDEFIEKSVSEPLASFSGNREEADNPNTGTGAFGFMLEPNKGKSVLEFQELMTV
ParentalFQLLHWNGSLKALRETKCSRQXXXXXXXXXXXXXXXXXXMALDWIMKR-ES-PGILSQELRMVLRELEEA
FQLLHWNGSL.A.RE...S.Q..................MAL.W.....ES.PG.LS.EL.....EL.EA
RetrocopyFQLLHWNGSLQAMRERPSSQQEVLAHYSPPALDDDIRHQMALHWVSRE<ESVPGALSRELASTEWELDEA
ParentalRKAGQELRFYKEKKEIVSLALTQIYN
...G..L.F.KEKK.I..LA..Q..N
RetrocopyWLGGKLLCFHKEKKDILMLAAGQLGN

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 1 .17 RPM 0 .78 RPM
SRP012922_cerebellum 1 .37 RPM 1 .92 RPM
SRP012922_heart 2 .09 RPM 0 .00 RPM
SRP012922_kidney 0 .82 RPM 0 .00 RPM
SRP012922_liver 2 .01 RPM 0 .00 RPM
SRP012922_lung 3 .82 RPM 0 .00 RPM
SRP012922_quadricep_muscle 0 .69 RPM 0 .17 RPM
SRP012922_spleen 4 .92 RPM 0 .00 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_2085 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000012335 1 retrocopy
retro_dnov_2085 ,
Equus caballus ENSECAG000000216431 retrocopy
Mus musculus ENSMUSG000000477861 retrocopy



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