RetrogeneDB ID: retro_osat_14

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 3:36204110..36204851(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS03G0857900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS03G0109300
• Aliases: None
• Description: None

Sequence

>retro_osat_14
ATGATGATGGAGAATAGCAGGGAGCAGCAGCCGGAGTCGTCGCCGGCGAACAACAATAGCAAGAAGAAGAAGAAGAAGAA
GACGGCGTCGCGGTTCCGGCGTGTGTGCGTGTTCTGCGGCAGCAGCCCCGGGAAGAAGGCGTCGTACCAGGTGGCCGCCG
TGCAGCTGGGGCAGCAGCTGGTGGAGCGCGGCATCGACCTGGTGTACGGCGGCGGCAGCGTTGGGCTGATGGGGCTGGTG
TCCCGCGCCGTCCACGGAGGCGGCGGGCACGTGGTGGGCGTGGTGCCCAATGGCGTGCTGCCACGCGAGCTGATCGGCGA
GACGCTGGGGGAGGTGAGGGCGGTGGGAAGCATGCACCAGCGGAAGGCGGAGATGGCGCGGGAGTCGGACGCCTTCATCG
CCCTCCCCGGCGGCTACGGCACGCTGGAGGAGCTCCTCGAGGTCATCACCTGGGCTCAGCTCCGCATCCACCACAAGCCC
GTCGGCCTCCTCAACGTCGACGGCTACTACGACTCCCTGCTCGCCTTCATCGACAAGGCCGTCCACGAAGGCTTCGTCTC
GCCGCCCGCCCGCCGCATCATCGTCGCCGCACCCACCGCCTCCGACCTGCTCTGCAAGCTCGAGGAATACGTGCCGCCGC
CGCACGACGCCACCGCCCTGAAGCTCACCTGGGAGATGTCCACCGTATCGGAGCAGCACGCCGGAAGCATCTACTCCCCC
AAGCCCGACATGGCACGCTAG

Alignment

ORF - retro_osat_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.73 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQQQQQQQESRFKRTCVFCGSSQGNKTTYRDAAVDLAKELVARGIDLVYGGGSIGLMGLVSQAVYDGGRH
          .........SRF.R.CVFCGSS.G.K..Y..AAV.L...LV.RGIDLVYGGGS.GLMGLVS.AV..GG.H
Retrocopy KKKKKKKTASRFRRVCVFCGSSPGKKASYQVAAVQLGQQLVERGIDLVYGGGSVGLMGLVSRAVHGGGGH

Parental  VIGVIPKTLMTPEIIGETVGEVRPVSDMHQRKAEMARQSDAFIALPGGYGTLEELLEVITWAQLGIHHKP
          V.GV.P......E.IGET.GEVR.V..MHQRKAEMAR.SDAFIALPGGYGTLEELLEVITWAQL.IHHKP
Retrocopy VVGVVPNGVLPRELIGETLGEVRAVGSMHQRKAEMARESDAFIALPGGYGTLEELLEVITWAQLRIHHKP

Parental  VGLLNVDGYYNSLLTFIDQAVEEGFISPSARRIIVSAPTAQELMDKLEEYV-PYHDRVASGLNWE
          VGLLNVDGYY.SLL.FID.AV.EGF.SP.ARRIIV.APTA..L..KLEEYV.P.HD..A..L.WE
Retrocopy VGLLNVDGYYDSLLAFIDKAVHEGFVSPPARRIIVAAPTASDLLCKLEEYVPPPHDATALKLTWE

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_14 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA03G0005200	1 retrocopy	retro_ogla_37,
Oryza sativa japonica	OS03G0109300	1 retrocopy	retro_osat_14 ,