RetrogeneDB ID: retro_osat_49

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 9:9567550..9568627(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS09G0325700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS03G0268600
• Aliases: None
• Description: None

Sequence

>retro_osat_49
ATGTCGATGGCGGAGGTGTGCTGTGATTCTGCGGTGGTGGTCGGGGCGGAGGCGGAGGCGAGGGCGAGGGCGCGCGCCGG
GAGGCGGCGGCGGGCGGGAGTTGAGGGGGCAGGGAGGTGGAACGCCACGGCGACGGCTGCGGGTGTGGCGGCGGAGGAGG
CCGCGACGAGGAAGCGGAGGGCGAGTGGTGGTGAGGCCGGGTTGGTGGTGGTGGCGAAGCGGCACGGGGCGGCGTCGGTC
GCCGGGAGGAGGAGGGAGATGGAGGACGCCGTGTCGCTGCGCGAGGCGTTCGCCGCGCCGGCGAACGGGGAGGTTGCGGC
GGCGAGGTGTGACTTCTACGGGGTGTTCGACGGGCACGGCTGCTCGCACGTGGCGGACGCGTGCAGGGAGCGGATGCACG
AGCTCGTCGCGGAGGAGATGGGCGCCGGGTCACCGGCGGCGGCGGCGCGCGAGCCGGCGTCTTGGACGGAGACGATGGAG
CGGAGCTTCGCGAGGATGGACGCCGAGGTGATCGCCGGCTGCCGAGCCGAGAGCGGCAGCTGCCGGTGCGAGGGGCAGAA
GTGCGACCACGTGGGGTCCACCGCGGTGGTGGCCGTCGTGGAGGAGAGCCGCGTCGTCGTCGCCAACTGCGGCGACTCCC
GCGCCGTGCTCTGCCGCGGCGGCGCGCCCGTGCAGCTATCCTCCGACCACAAGCCCGACCGCCCCGACGAGCTGGAGCGG
ATCGAGGCGGCCGGCGGCCGCGTCATCTTCTGGGAGGGCGCCCGTGTCCTCGGCGTCCTCGCCATGTCGCGCTCCATCGG
CGACGCCTACCTGAAGCCCTACGTCACCGCCGTGCCGGAGGTGACGGTGACCGGCAGGTCGGACTTCGACGAGTGCCTCA
TCCTCGCCAGCGACGGCCTCTGGGACGTCGTCAGCAACGAGGCCGCGTGCGAGGTGGCGCAGTCGTGCCTCCGCCGCGGC
AGGCAGCGGTGGTGCGCCGAGGCGGCGGCGGTGCTGACCAAGCTGGCCCTCGCTCGCCGCAGCTCCGACAACATCTCTGT
CGTCGTCGTCGATCTCCGGCGAGGCAACGCCTTGTAG

Alignment

ORF - retro_osat_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 53.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFGVFDGHGCSHVATSCGQRMHEIVVDEAGAAAGSAGLDEEARWRGVMERSFARMDAEAVASSRGSVAPA
          F.GVFDGHGCSHVA..C..RMHE.V..E.GA....A...E.A.W...MERSFARMDAE..A..R...A..
Retrocopy FYGVFDGHGCSHVADACRERMHELVAEEMGAGSPAAAAREPASWTETMERSFARMDAEVIAGCR---AES

Parental  PTCRCEMQLPKCDHVGSTAVVAVLGPRHVVVANCGDSRAVLCRGGAAIPLSCDHKPDRPDELERIHAAGG
          ..CRCE.Q..KCDHVGSTAVVAV.....VVVANCGDSRAVLCRGGA...LS.DHKPDRPDELERI.AAGG
Retrocopy GSCRCEGQ--KCDHVGSTAVVAVVEESRVVVANCGDSRAVLCRGGAPVQLSSDHKPDRPDELERIEAAGG

Parental  RVIFWDGARVFGMLAMSRAIGDSYLKPYVICDPEVRVMERKDGEDEFLILASDGLWDVVSNEVACNVVRA
          RVIFW.GARV.G.LAMSR.IGD.YLKPYV...PEV.V..R.D..DE.LILASDGLWDVVSNE.AC.V...
Retrocopy RVIFWEGARVLGVLAMSRSIGDAYLKPYVTAVPEVTVTGRSD-FDECLILASDGLWDVVSNEAACEVAQS

Parental  CLRSSGRR
          CLR....R
Retrocopy CLRRGRQR

Legend:

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

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_49 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_56081	1 retrocopy	retro_hvul_16,
Oryza punctata	OPUNC03G11550	1 retrocopy	retro_opun_31,
Oryza sativa japonica	OS03G0268600	1 retrocopy	retro_osat_49 ,
Sorghum bicolor	Sb01g039890	1 retrocopy	retro_sbic_41,
Setaria italica	Si036015m.g	1 retrocopy	retro_sita_14,