RetrogeneDB ID: retro_opun_45

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 12:19524286..19524598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G26460
• Aliases: None
• Description: None

Sequence

>retro_opun_45
ATGGTAGAAGGGTCAGCTCAAGGACTCCACACCGGTAAGGTGATGCAGGAAGCAACACAGTGGCTCGGGAGCATGCGGAG
ACCTTGGTGCGTGAGATGTAGGCACGGTGGTCTCTGGGACTATCGCGTTAGATCGGCAACTTGGCAAGGGAACGAAGACG
AACATCTGCTATTTCAGATTGCCAATGTTGGCACCATTGAAAGCCTAGACTACGAGCTATAAGTCCCTCAAACCCTGTGT
CTTTTCTTAATCTACTCCGTACATGTGGAAATTTTGATCTTTATTATATCTAATGTCTTTGTTCTTGAGTCT

Alignment

ORF - retro_opun_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.42 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVEGSAQGIHTGKVVQEATQWPGSMWRPWCVRFRHGGLRDYHVRSATWQGNDDEHLPHQIANVGPIESLD
          MVEGSAQG.HTGKV.QEATQW.GSM.RPWCVR.RHGGL.DY.VRSATWQGN.DEHL..QIANVG.IESLD
Retrocopy MVEGSAQGLHTGKVMQEATQWLGSMRRPWCVRCRHGGLWDYRVRSATWQGNEDEHLLFQIANVGTIESLD

Parental  YEHYSGAVLTIY--YHIWCVVVIRLFENVGEVET
          YE......L.....Y.......I....NV...E.
Retrocopy YEL*VPQTLCLFLIYSVHVEILIFIISNVFVLES

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_45 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC03G26460	1 retrocopy	retro_opun_45 ,