RetrogeneDB ID:

retro_dnov_1307

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_179219:0..1312(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000025699
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SPG20
Ensembl ID:ENSDNOG00000015441
Aliases:None
Description:spastic paraplegia 20 (Troyer syndrome) [Source:HGNC Symbol;Acc:18514]


Retrocopy-Parental alignment summary:






>retro_dnov_1307
AACGGAAGCACCTCCGATGCCAGCGTGGGGTCGGCACCTGGGCCGGCGCCTCTGGGCAGGCCACCTCCCAGCTGCCCCGC
AGAGGCGCCTCCTGCTTACACCCCTCAGGCCGCCGAGGGCCACTACACTGTGTCCTACGGGACAGATTCGGGAGAATATT
CCTCAGTTGGGGAGAACTTCTACAGGAACCATTCTCAGCCACCTCCTCTTGAGACCCTGGGGCTTGATGCCGATGAGTTG
ATCTTGATACCAAATGGAGTACAGATTTTTTTTGTAAACCCAGCAGGGGAAGGTTAGCGCACCTTCATATCCTGGTTATC
TTCGCATTGTGAGGTTCTTGGATAATTCTCTCGATACGGTTCTGAACCGTCCTCCTGGGTTTCTTCAGGTTTGTGACTGG
TTATATCCTCTAGTTCCTGATAGATCTCCAGTTCTGAAATGTACTGCAGGAGCCTACATGTTTCCTGATACAATGTTACA
AGCATCAGGGTGCTTTGTGGGGGTCGTCTTGTCATCTGAATTACCTGAAGATGACAGAGAACTCTTTGAGGATCTTTTAA
GACAAATGTCTGACCTTCGGCTCCAGGCCAACTGGAATAGGGCTGAAGGAGAAGCGAATTCCAATCCCTGGAAGAATGAG
GCACTCCTCTGACCAGTTAAAGGAAGCCTCTGGCACTGATGTGAGACAGTTGGGTCCTTCTTTGGACCAAGGCAATAAGG
ATGTACGTCATAAAGAAAAACGTGGGAAAAAGGCTAAGAATACTTCAAGTGAAGAAGTTAATCTGAGTCACATTGTACCC
TGTGAACCAGTATCAGAAGAAAAAGCAAAGGAATTACCTGAATGGAGTGAGAAAGTGGCTCAAAACATTTTGTCAGGTGC
TTCCTGGGTGAGTTGGGGCTTAGTTAAAGGTGCTGAATTTACTGGCAAAGCAATTCAGAAAGGTGCTTCTAAACTCCGAG
AACGTATTCAACCAGAAGAAAAACCCGTGGAAGTTAGCCCAGCTGTGAGCAGGGGACTTCACCTAGCAAAGCAGGCTACA
GGAGGAGCAGCGAAAGTCAGCCAGTTCCTGGTTGACGGAGTTTGCACTGTAGCAAATTGTGTTGGAAAAGAACTAGCTCC
ACATGTCAAGAAGCATGGAAGTAAACTTGTTCCAGAGTCTCTTAAAAAAGACAAAGATGGGAAGTCCCCTCTGGATGGTG
CGCTGGTCATAGCGGCAAGTAGTGTTCAAGGATTTTCAACCATCTGGCAGGATTGGAATGTGCAGCTAAATGCATTGTTA
ACAATGTTTCTGCAGAGACTGTACAAACTGTC

ORF - retro_dnov_1307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.34 %
Parental protein coverage: 65.37 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalNGSTSDASVGSAPGPAPLGRPPPSCPAEAPPAYTPQAAEGHYTVSYGTDSGEYSSVGENFYRNHSQPPPL
NGSTSDASVGSAPGPAPLGRPPPSCPAEAPPAYTPQAAEGHYTVSYGTDSGEYSSVGENFYRNHSQPPPL
RetrocopyNGSTSDASVGSAPGPAPLGRPPPSCPAEAPPAYTPQAAEGHYTVSYGTDSGEYSSVGENFYRNHSQPPPL
ParentalETLGLDADELILIPNGVQIFFVNPAGE-VSAPSYPGYLRIVRFLDNSLDTVLNRPPGFLQVCDWLYPLVP
ETLGLDADELILIPNGVQ...VNPAGE.VSAPSYPGYLRIVRFLDNSLDTVLNRPPGFLQVCDWLYPLVP
RetrocopyETLGLDADELILIPNGVQXXXVNPAGE>VSAPSYPGYLRIVRFLDNSLDTVLNRPPGFLQVCDWLYPLVP
ParentalDRSPVLKCTAGAYMFPDTMLQASGCFVGVVLSSELPEDDRELFEDLLRQMSDLRLQANWNRAEGE-SEFQ
DRSPVLKCTAGAYMFPDTMLQASGCFVGVVLSSELPEDDRELFEDLLRQMSDLRLQANWNRAEGE.SEFQ
RetrocopyDRSPVLKCTAGAYMFPDTMLQASGCFVGVVLSSELPEDDRELFEDLLRQMSDLRLQANWNRAEGE<SEFQ
Parental-IPGRMRHSSDQLKEASGTDVRQLGPSLDQGNKDVRHKEKRGKKAKNTSSEEVNLSHIVPCEPVSEEKAK
.IPGRMRHSSDQLKEASGTDVRQLGPSLDQGNKDVRHKEKRGKKAKNTSSEEVNLSHIVPCEPVSEEKAK
Retrocopy<IPGRMRHSSDQLKEASGTDVRQLGPSLDQGNKDVRHKEKRGKKAKNTSSEEVNLSHIVPCEPVSEEKAK
ParentalELXXXXXXXXXXXXXXASWVSWGLVKGAEFTGKAIQKGASKLRERIQLEEKLVEVSSAVSRGLHLAKQAT
EL..............ASWVSWGLVKGAEFTGKAIQKGASKLRERIQ.EEK.VEVS.AVSRGLHLAKQAT
RetrocopyELPEWSEKVAQNILSGASWVSWGLVKGAEFTGKAIQKGASKLRERIQPEEKPVEVSPAVSRGLHLAKQAT
ParentalGGAAKVSQFLVDGVCTVANCVGKELAPHVKKHGSKLVPESLKKDKDGKSPLDGALVIAASSVQGFSTVWQ
GGAAKVSQFLVDGVCTVANCVGKELAPHVKKHGSKLVPESLKKDKDGKSPLDGALVIAASSVQGFST.WQ
RetrocopyGGAAKVSQFLVDGVCTVANCVGKELAPHVKKHGSKLVPESLKKDKDGKSPLDGALVIAASSVQGFSTIWQ
Parental-GLECAAKCIVNNVSAETVQTV
.GLECAAKCIVNNVSAETVQTV
Retrocopy<GLECAAKCIVNNVSAETVQTV

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 9 .33 RPM 46 .28 RPM
SRP012922_cerebellum 13 .61 RPM 73 .13 RPM
SRP012922_heart 3 .25 RPM 31 .09 RPM
SRP012922_kidney 9 .58 RPM 57 .50 RPM
SRP012922_liver 9 .13 RPM 39 .63 RPM
SRP012922_lung 19 .40 RPM 82 .17 RPM
SRP012922_quadricep_muscle 10 .21 RPM 42 .75 RPM
SRP012922_spleen 15 .80 RPM 68 .45 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_1307 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 ENSDNOG00000015441 1 retrocopy
retro_dnov_1307 ,


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