RetrogeneDB ID: retro_osat_28

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 12:26913260..26913794(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS12G0628600
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS12G0629600
• Aliases: None
• Description: None

Sequence

>retro_osat_28
ATGGCGTCTCCGGCCACCTCTTCCGCTGTCCTCGTCGTCGTCCTGGTGGCGACCCTCGCCGCCGGTGGCGCCAACGCGGC
GACCTTCACCATCACCAACCGGTGCTCGTTCACGGTGTGGCCGGCGGCGACGCCGGTGGGCGGCGGCGTGCAGCTGAGCC
CGGGGCAGACGTGGACCATCAACGTGCCCGCCGGGACCAGCTCCGGCAGGGTGTGGGGCCGCACGGGCTGCAGCTTCGAC
GGCTCCGGCCGCGGCAGCTGCGCCACCGGCGACTGCGCCGGCGCCCTGTCGTGCACCCTCTCCGGCCAGAAGCCGCTGAC
GCTGGCGGAGTTCACCATCGGCGGCAGCCAGGACTTCTACGACCTGTCGGTGATCGACGGCTACAACGTCGCCATGAGCT
TCTCCTGCAGCTCCGGCGTGACGGTCACCTGCAGGGACAGCCGCTGCCCCGACGCTTACCTGTTCCCCGAAGACAACACC
AAGACACACGCCTGCAGCGGCAACAGCAACTACCAAGTCGTCTTCTGCCCATAA

Alignment

ORF - retro_osat_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPATSSAILVVVLVASLAAGGANAATFTITNRCSFTVWPAATPVGGGRQLSPGDTWTINVPAGTSSGR
          MASPATSSA.LVVVLVA.LAAGGANAATFTITNRCSFTVWPAATPVGGG.QLSPG.TWTINVPAGTSSGR
Retrocopy MASPATSSAVLVVVLVATLAAGGANAATFTITNRCSFTVWPAATPVGGGVQLSPGQTWTINVPAGTSSGR

Parental  VWGRTGCSFDGSGRGSCATGDCGGALSCTLSGQPPLTLAEFTIGGSQDFYDLSVIDGYNLPMSFSCSSGV
          VWGRTGCSFDGSGRGSCATGDC.GALSCTLSGQ.PLTLAEFTIGGSQDFYDLSVIDGYN..MSFSCSSGV
Retrocopy VWGRTGCSFDGSGRGSCATGDCAGALSCTLSGQKPLTLAEFTIGGSQDFYDLSVIDGYNVAMSFSCSSGV

Parental  TVTCRDSRCPDAYLFPEDNTKTHACGGNSNYQVVFCP
          TVTCRDSRCPDAYLFPEDNTKTHAC.GNSNYQVVFCP
Retrocopy TVTCRDSRCPDAYLFPEDNTKTHACSGNSNYQVVFCP

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_28 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa japonica	OS12G0629600	1 retrocopy	retro_osat_28 ,