RetrogeneDB ID: retro_opun_4

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 3:29042293..29042803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC03G26800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G37500
• Aliases: None
• Description: None

Sequence

>retro_opun_4
ATGGCGAAGAAAGCAACACCCAACGCCGCCGCAGCCGGCAACTGCAAGTACTGGCTGCTCAAGACGGAGCCGGGGGAGTG
GTCGTGGTCCGACCAGGCGCGCGCCCCCGGCGGCGGCGTCGCGCCGTGGGACGGCGTCCGCAACCGCCAGGCCATCAACA
GCCTCCGCGCCATGCGGGAAGGCGACCGCTGCCTCTTCTACCACTCCGGCGCCGGGGCCGCCTCCCGCCGCGTCGTCGGC
GTTGTGGAGGTCGCCAGGGAGTGGTACGAGGGGGAGGCGGCGAGCGGCGGCGCCGTTGACGTCCGCGCGGTGGGGGAGTT
CCGGCGGCCGGTGGCGCTCGGGGACATCAAGAAGGCGGCGGGTGGCGGCGAGGTGGAGGGGATGAGGGAGTTCGCGCTGC
TCCGGCAGCCTCGGCTGTCGGTGATGCCCGTGCCGGCGAAGGTCTGGGATTGGATTTGCGAGATGGGAGGGGGCTTTGTG
CAAGATGGGGAGGATGAAGATGAATGCTGA

Alignment

ORF - retro_opun_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.82 %
• Parental protein coverage: 50.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLAVANRRRSTPRRKSSGDEREGRDEAKRQASMSHILTNAPVARGLYEGEAASGSAVDVRAVGEFQLPVA
          W..V.NR......R......R.........A..........VAR..YEGEAASG.AVDVRAVGEF..PVA
Retrocopy WDGVRNRQAINSLRAMREGDRCLFYHSGAGAASRRVVGVVEVAREWYEGEAASGGAVDVRAVGEFRRPVA

Parental  LGDIKKAKGGEEVEGMREFALLRRPRLSVMPV
          LGDIKKA.GG.EVEGMREFALLR.PRLSVMPV
Retrocopy LGDIKKAAGGGEVEGMREFALLRQPRLSVMPV

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_4 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	OPUNC01G37500	1 retrocopy	retro_opun_4 ,