RetrogeneDB ID:

retro_osat_21

Retrocopy
location
Organism:Rice subsp. japonica (Oryza sativa japonica)
Coordinates:1:43244270..43245254(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OS01G0978400
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OS03G0818200
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_osat_21
ATGGAGGAGGAGCGGCGCGTGCTCGTGACCGGCGGCAATGGTTTCATCGGATCCTGGATCGTGCGGATCCTTCTCGCACG
CGGGTACGCCGTGACCGCAACCTACCAGCCGGGCACGGACGCTGCGCACCTCCTCGCCCTCGACGACGAAAGGCTCCTCC
TGCTCCCCGCCGACCTGCTTGATGCGGGCGCCATCTCCGCGGCGGCGGCAGCGGGCGGGGGCTGCCGGGCGGGCGTGCTG
CACGTGGCCTCCCCGTGCACGCTGGCTGACCCGCGGGATCCGCAGGCCGAACTGGTGGAGCCGGCGGTGCGGGGCACGCT
GCACGTGCTGGAGGCGGCGCGGGGCGCGGGAGCGCGGCGCGTGGTGGTGACGTCCTCCATCTCAGCCATGGTGCCCAACC
CGGGGTTGGCGGCGGGAGAGCTCGTCGACGAGCGAAGCTGGACGGACATGGAATTCTGCAAGGCCCGGGGCAAGTGGTAC
CCGGTGTCCAAGACGCTGGCCGAGAGGGCGGCGTGGGAGTACGCGGCGCGGTGGCCCGGCTTCGAGTTGGCCACCATCCT
GCCGTCGACATGCCTCGGCCCGCTCCTGCAGCCCACCCTGAACGCCAGCTCTGTCGTGCTGCAGCGCCTCTTGCAGGGCT
CCACGGACGACCAGGCGGACTACTGGCTCGGCGCCGTCCACGTCCGCGACGTCGCCGCCGCCCACCTCCTGCTGCTCGAG
GCTCCCACCGTCTCCGGGAGGTACCTCTGCACCAACGGCATCTACCAGTTCAGCGACTTCGCACGGCTAGCTGCCAGGAT
CTGCCCCGCGTACGCCCACGCCATCCACCGCTTCGAGGAGGGGACTACACAACCGTGGCTCGTGCCGCGCGACGCCCGTG
ACGCAGCACGCCGGCTCCTCGACCTCGGCCTCGTCCTCACTCCCCTCGAGGAGGCCATCAAGGACGCGGAGAAGAGTCTC
ACCGATAAATGCTTCCTTCCTTGA

ORF - retro_osat_21 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.1 %
Parental protein coverage: 69.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTDHLHALAAAGGGEGRRLRVFPGDLLDGAALLAAAR---GC-SGVFHLASPCIVDRVLDPQAQLMVPAVE
TD..H.LA........RL...P.DLLD..A..AAA....GC..GV.H.ASPC......DPQA.L..PAV.
RetrocopyTDAAHLLAL----DDERLLLLPADLLDAGAISAAAAAGGGCRAGVLHVASPCTLADPRDPQAELVEPAVR
ParentalGTLNVLRAAKDAGGVRRVVVTSSISAIVPSPGWPAGEVRDERCWTDLDYCEKNGVWYPASKTLAEKAAWK
GTL.VL.AA..AG..RRVVVTSSISA.VP.PG..AGE..DER.WTD...C...G.WYP.SKTLAE.AAW.
RetrocopyGTLHVLEAARGAGA-RRVVVTSSISAMVPNPGLAAGELVDERSWTDMEFCKARGKWYPVSKTLAERAAWE
ParentalFAEE-NGLDVVVVNPGTVMGLVIPPTINASMAMLVRLLEGCTEEYADFYMGPVHVEDVALAHILLYENPS
.A....G.......P.T..G....PT.NAS...L.RLL.G.T...AD...G.VHV.DVA.AH.LL.E.P.
RetrocopyYAARWPGFELATILPSTCLGPLLQPTLNASSVVLQRLLQGSTDDQADYWLGAVHVRDVAAAHLLLLEAPT
ParentalASGRHLCVQSIAHWSDFASKVAELYPEY
.SGR.LC...I...SDFA...A...P.Y
RetrocopyVSGRYLCTNGIYQFSDFARLAARICPAY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Oryza sativa japonica was not studied using RNA-Seq expression data.
Oryza sativa japonica was not studied using ChIP-Seq data.
Oryza sativa japonica was not studied using EST data.
Oryza sativa japonica was not studied using FANTOM5 data.
retro_osat_21 was not experimentally validated.

Retrocopy orthology:
Oryza sativa japonica 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
Oryza sativa indicaBGIOSGA0138251 retrocopy
Oryza punctata OPUNC03G360001 retrocopy
Oryza sativa japonicaOS03G0818200 1 retrocopy
retro_osat_21 ,



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