RetrogeneDB ID: retro_osat_60

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 11:2435960..2436509(-)
• Located in intron of: OS11G0151800

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS04G0410700
• Aliases: None
• Description: None

Sequence

>retro_osat_60
GACGTGCCCGGCGAACACCGCGTCCACGCGCGCGCCGCGGAGGAGCTCCTCCATGGCGGCGCGCATGGCGTCGCCCTCGC
CCCGGTGCGCTTCGTTGCTGTTGTACCACGGCGCGTGCACCAGCGCCACCACGAACGCCGCCCTGGCGCGGTCGACGGCG
GCGAGGTCGCGGCGCAGCCACCGGTGCTGCGCCGAGCCGGCGGCGTAGTCGGCGTAGGAGCCCAGCATGATGACGTGCAC
GGCGCCGCCGGCGACGTCGAAGGAGTAGTAGAGGTTGGACCCCGACGGCGACGCGCCGGCATCGAACGGCATGCGCCACC
GCGCGTTGTACGCCTTGAACGCGTGGGGCTCCACGAGGGGGATCCTCTCCACCTCGTGGTTCCCCTGCGTCACCATCCAT
GGCCGCGCGCTCGCCAGCGGCTCCACGAGGCGGCCGTACGTGTCCCACCTCGGCTGGTACAGGTCGGCGTACGACAGGTC
GCCGGGGAGCAGCAGCATGTCGTAGTCGTCGCCGCCGATGTGCCGGAGCGTCGACTCCGTCCATCCCGT

Alignment

ORF - retro_osat_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.43 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVAGVGAPRRRAGDPALHGLPHGLALPLVRRVRVVPGRVQQHHDPGRRAAVDGGEVAGQPPVLLRARVEV
          .V.G......RA....LHG..HG.AL..VR.V.VVP.RV.Q.H...R..AVDGGEVA.QPPVL.RA...V
Retrocopy DVPGEHRVHARAAEELLHGGAHGVALAPVRFVAVVPRRVHQRHHERRPGAVDGGEVAAQPPVLRRAGGVV

Parental  GVRAEHDDVDGAAGGVEGVVEAGPRA--ALLVRHPPPRGVRRERPRPARERHRGLHLVVPFGDHPWPPAR
          GV.A.HDDV.GAAG.VEGVVE.GPR...A...RH.PPR.VR.E..R........LHLVVP...HPWP.AR
Retrocopy GVGAQHDDVHGAAGDVEGVVEVGPRRRRAGIERHAPPRVVRLE--RVGLHEGDPLHLVVPLRHHPWPRAR

Parental  VLLHEPAERVPQRLLGVGVGQASPPTAHLAPLTLAACGHGVRPRR
          ..LHE.A.RVP.RL..VGV.Q......H.............RP.R
Retrocopy QRLHEAAVRVPPRLVQVGVRQVAGEQQHVVVVAADVPERRLRPSR

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_60 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa japonica	OS04G0410700	1 retrocopy	retro_osat_60 ,