RetrogeneDB ID:

retro_olon_7

Retrocopy
location
Organism:Longstamen rice (Oryza longistaminata)
Coordinates:KN539288.1:76677..77526(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:KN539288.1_FG012
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:KN540828.1_FG001
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_olon_7
ATGGCTGCAGGCAGCGGCAGCGGCAGCGGCAGCAATCCTAAGGACTACCAGGATCCTCCTCCCGCGCCGCTGGTGGACAC
CGGCGAGCTAGGTAAGTGGTCACTGTATCGCGCCGCCATTGCGGAGTTCACAGCCACGCTGCTGTTGGTGTGCATCAGTG
TGAGCACAGTGATCGGTGAGAAGCGGCAGTCGGGCGAGGGCGGCGCCGGCGTGCTTGGCATTGCCTGGGCCTTTGGTGGC
CTCATCTTCGTGCTGGTGTACTGCACCGCTGGCATCTCCGGGGGGCACATGAACCCAGCCGTGACCTTCGCCATGGTGCT
CGCGCGAAGGGTGTCGCTGCCGCGAGCGGCGCTGTACACGATGGCGCAGTGCGTGGGCGCCGTGTGCGGCGCAGGGCTCG
CCAGGGCGATGCACGGTGGCGGGCAGTACGCGCGGCACGGCGGAGGCGCCAACGAGCTGGCGGCGGGCTACTCGGCGGGG
GCAGGGGTGGCGGCGGAGATGGTGGGCACGTTCGTGCTGGTGTACACGGTGTTCTCGGCGACGGACCCGAAGCGGAAGGC
CAGGGACTCTCACGTGCCGGTGCTGGCGCCGCTTCCCATCGGGCTGGCTGTGCTGGTTGTGCACCTTGCCACCATCCCCA
TCACCGGCACTGGCATCAACCCCGCCCGCAGCCTTGGCCCCGCCCTCGTCCTCGGCCTCGGCACCACCACCAAGGCCTGG
TCCCACCTCTGGATCTTCTGGGTGGGCCCCTTCGCCGGCGCCGCCGCCGCAATGATCTACCATCACTACATCCTCAGGGG
CGCTGCCGCCAAGGCCTTCGCCTCCTCCTACCGACCACCCCATTTTTAA

ORF - retro_olon_7 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.17 %
Parental protein coverage: 92.91 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPKDYTDPPPAPLFDVGELRLWSFYRALIAEFIATLLFLYITVATVIGYKVQSSADQCGGVGTLGIAWAFG
PKDY.DPPPAPL.D.GEL..WS.YRA.IAEF.ATLL...I.V.TVIG.K.QS.....GG.G.LGIAWAFG
RetrocopyPKDYQDPPPAPLVDTGELGKWSLYRAAIAEFTATLLLVCISVSTVIGEKRQSGE---GGAGVLGIAWAFG
ParentalGMIFILVYCTAGISGGHINPAVTFGLLLARKVSVIRAVMYIVAQCLGGIVGVGIVKGIMKH-QYNANGGG
G.IF.LVYCTAGISGGH.NPAVTF...LAR.VS..RA..Y..AQC.G...G.G.........QY...GGG
RetrocopyGLIFVLVYCTAGISGGHMNPAVTFAMVLARRVSLPRAALYTMAQCVGAVCGAGLARAMHGGGQYARHGGG
ParentalANMVASGYSTGTALGAEIIGTFVLVYTVFSATDPKRNARDSHVPVLAPLPIGFAVFMVHLATIPITGTGI
AN..A.GYS.G....AE..GTFVLVYTVFSATDPKR.ARDSHVPVLAPLPIG.AV..VHLATIPITGTGI
RetrocopyANELAAGYSAGAGVAAEMVGTFVLVYTVFSATDPKRKARDSHVPVLAPLPIGLAVLVVHLATIPITGTGI
ParentalNPARSIGAAVIY---NQKKAWDDHWIFWAGPFIGALAAAAYHQYILRAAAIKALGS
NPARS.G.A.........KAW...WIFW.GPF.GA.AA..YH.YILR.AA.KA..S
RetrocopyNPARSLGPALVLGLGTTTKAWSHLWIFWVGPFAGAAAAMIYHHYILRGAAAKAFAS

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






Oryza longistaminata was not studied using RNA-Seq expression data.
Oryza longistaminata was not studied using ChIP-Seq data.
Oryza longistaminata was not studied using EST data.
Oryza longistaminata was not studied using FANTOM5 data.
retro_olon_7 was not experimentally validated.

Retrocopy orthology:
Oryza longistaminata 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 11 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Oryza sativa indicaBGIOSGA0093621 retrocopy
Oryza longistaminata KN540828.1_FG001 1 retrocopy
retro_olon_7 ,
Leersia perrieri LPERR04G034301 retrocopy
Oryza brachyantha OB0038G100901 retrocopy
Oryza barthii OBART04G050501 retrocopy
Oryza glumaepatula OGLUM04G042401 retrocopy
Oryza meridionalis OMERI04G050101 retrocopy
Oryza nivara ONIVA04G033001 retrocopy
Oryza punctata OPUNC04G043101 retrocopy
Oryza rufipogon ORUFI04G057801 retrocopy
Oryza sativa japonicaOS04G02334001 retrocopy



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