RetrogeneDB ID:

retro_dnov_1089

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_145052:3994..4481(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA3
Ensembl ID:ENSDNOG00000004077
Aliases:None
Description:proteasome (prosome, macropain) subunit, alpha type, 3 [Source:HGNC Symbol;Acc:9532]


Retrocopy-Parental alignment summary:






>retro_dnov_1089
ATGAGCTCTATCTGCACTGAGTATGACCTGTCAGCCTCTACACTCCCTCCTGACGGGAGAGTTTTTCTAGTTGAATATGC
TATGAAGGCTGTGGAAAATAGTAGTACAGCTATTGGAATCAGATGTAAAGATGGTGTTGTCTTCGGAGTAGAAAAAATTA
GTCCTTTCTAAACTTTATGAAGAAGGTTCCAACAAACGGCTTTTTAATGTTGATCAGCATGCTGGAATGGCGGTAGTAGG
TTTGTTGGCAGATGCTCGTTCTTTAGCAGACATAGCAAGAGAAGAAGCTTCTAACTTTAGATCTAACTTTGGCTGTAACA
TTCCACTCAAACATCTTGCAGATAGAGTGGCCATGTATGTTCATGCCCATACACTGTACAGTGCTGTTAGACCTTTTGGA
TGCAGTTTCATGTTCGGGTCTTACATTGTGAATGATGGTGCACAACTCTACATGATTGATCCATTGGGTGTTTCATATGG
TTATTGG

ORF - retro_dnov_1089 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.41 %
Parental protein coverage: 63.53 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEK-LVLSKLYEEGSNKRLFN
MSSI.T.YDLSAST..PDGRVF.VEYAMKAVENSSTAIGIRCKDGVVFGVEK.LVLSKLYEEGSNKRLFN
RetrocopyMSSICTEYDLSASTLPPDGRVFLVEYAMKAVENSSTAIGIRCKDGVVFGVEK>LVLSKLYEEGSNKRLFN
ParentalVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLG
VD.H.GMAV.GLLADARSLADIAREEASNFRSNFG.NIPLKHLADRVAMYVHA.TLYSAVRPFGCSFM.G
RetrocopyVDQHAGMAVVGLLADARSLADIAREEASNFRSNFGCNIPLKHLADRVAMYVHAHTLYSAVRPFGCSFMFG
ParentalSYSVNDGAQLYMIDPSGVSYGYW
SY.VNDGAQLYMIDP.GVSYGYW
RetrocopySYIVNDGAQLYMIDPLGVSYGYW

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 46 .09 RPM
SRP012922_cerebellum 0 .00 RPM 24 .19 RPM
SRP012922_heart 0 .00 RPM 32 .72 RPM
SRP012922_kidney 0 .00 RPM 42 .71 RPM
SRP012922_liver 0 .00 RPM 30 .81 RPM
SRP012922_lung 0 .00 RPM 32 .53 RPM
SRP012922_quadricep_muscle 0 .00 RPM 33 .41 RPM
SRP012922_spleen 0 .00 RPM 43 .95 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_1089 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 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000152871 retrocopy
Callithrix jacchus ENSCJAG000000187321 retrocopy
Dasypus novemcinctus ENSDNOG00000004077 27 retrocopies
Dipodomys ordii ENSDORG000000021671 retrocopy
Homo sapiens ENSG000001005671 retrocopy
Gorilla gorilla ENSGGOG000000158141 retrocopy
Macaca mulatta ENSMMUG000000035092 retrocopies
Monodelphis domestica ENSMODG000000078391 retrocopy
Mustela putorius furoENSMPUG000000061262 retrocopies
Mus musculus ENSMUSG000000600733 retrocopies
Nomascus leucogenys ENSNLEG000000130921 retrocopy
Oryctolagus cuniculus ENSOCUG000000103161 retrocopy
Otolemur garnettii ENSOGAG000000003822 retrocopies
Ochotona princeps ENSOPRG000000028352 retrocopies
Pongo abelii ENSPPYG000000058552 retrocopies
Pan troglodytes ENSPTRG000000063901 retrocopy
Rattus norvegicus ENSRNOG000000078511 retrocopy
Sorex araneus ENSSARG000000026702 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000135391 retrocopy
Tupaia belangeri ENSTBEG000000169101 retrocopy
Tursiops truncatus ENSTTRG000000135261 retrocopy



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