RetrogeneDB ID: retro_opun_46

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 4:30258800..30259109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G32810
• Aliases: None
• Description: None

Sequence

>retro_opun_46
TTCGACGCGTTCGCGGACGCGCAGGGGGAGGACGCCGCCGCCGTCGGCGCCAGCGACTACGTGCACATCCGCGTGCAGCA
GCGCAATGGCCGGAAGACGCTGACCACCGTGCAGGGGCTCAGCGGCGAGTACAACTACGCCAAGGTGCTCCGCGACCTCA
AGCGGGAGCTCTGCTGCAACGGCACCGTCGTGGAGGACAAGGAGCTCGGCAAGATCATCCAGCTGCAGGGCGACCACCGG
AACACCGTCTGCGCCTTCCTCGCCAAGGCCGGCATGGTCAACAAGGACAAGATCAAGGTCCACGGGTTC

Alignment

ORF - retro_opun_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.46 %
• Parental protein coverage: 90.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDPFAEANAEDSSVGAGSKDYVHVRIQQRNGRKSLTTVQGLKKEYSYNKILKDLKKEFCCNGTVVQDPEL
          FD.FA.A..ED.....G..DYVH.R.QQRNGRK.LTTVQGL..EY.Y.K.L.DLK.E.CCNGTVV.D.EL
Retrocopy FDAFADAQGEDAAA-VGASDYVHIRVQQRNGRKTLTTVQGLSGEYNYAKVLRDLKRELCCNGTVVEDKEL

Parental  GQVIQLQGDQRKNVATFLVQAGIVKKESIKIHGF
          G..IQLQGD.R..V..FL..AG.V.K..IK.HGF
Retrocopy GKIIQLQGDHRNTVCAFLAKAGMVNKDKIKVHGF

Legend:

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

Expression

RNA-Seq

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_46 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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
Brachypodium distachyon	BRADI2G52330	1 retrocopy	retro_bdis_37,
Oryza punctata	OPUNC01G32810	1 retrocopy	retro_opun_46 ,