RetrogeneDB ID: retro_ogla_10

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 7:13305349..13305871(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA07G0117200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA03G0415200
• Aliases: None
• Description: None

Sequence

>retro_ogla_10
ATGCCTGCACGCAAGTCCCTCACTCACAAGTCCGAACGCGCTCGGGATCGGTCTCCCACTCCTTCTCCATCCTCCGCGGA
GGACTCGGACCATGCTTGGTCCAGGAAAGGGGAAGAGGAGACCGGCCCTCAGGTAGCACGTGTTCCTCGGGGTTCCACTC
AGCCTCCTCCCACTCGTGAGCGTCCCTCTCCTATGGCTCGTCGTGAGCCGTCTCCCTTATTCCGCATTCTGCGAAGTCTC
TTTGACCTTTGCGCCGCGGAGGCCAAAAAGAACCGCAGAATGCGGAATGGGATCAAGAAGACGGCTCGGCGCATCAAGAA
CATACAGGCGCAACTCAATGAGCATTTTCACGTGGATGTCCCTCCCTCCCCACCGGGCTTTGAGGCCGAGCCCGATGAGC
CTAAGGAGGAAGAGATCGAGGATCCTTTTGCTGGGATACCTCTGGACTACGATTTCTTTGGTTTTGGCCATGGCTATGGC
TATCCTCCTCCAGAGGATCCTCCTCAGGCGCCCTTCGCTTGA

Alignment

ORF - retro_ogla_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPRKQTSRKSKRSRDRSPTPSPSSHEDSDHDWSGGEEEETGPQVANVPRGSSLPPESAERPSSMARREP
          MP.RK....KS.R.RDRSPTPSPSS.EDSDH.WS...EEETGPQVA.VPRGS..PP...ERPS.MARREP
Retrocopy MPARKSLTHKSERARDRSPTPSPSSAEDSDHAWSRKGEEETGPQVARVPRGSTQPPPTRERPSPMARREP

Parental  SPLFRILRTLFGLCSVEAKKNRRLRNLAKKTARDVKYLKARYHEDHHIDIPPSPPGFEAELDEPEEEEIE
          SPLFRILR.LF.LC..EAKKNRR.RN..KKTAR..K...A...E..H.D.PPSPPGFEAE.DEP.EEEIE
Retrocopy SPLFRILRSLFDLCAAEAKKNRRMRNGIKKTARRIKNIQAQLNEHFHVDVPPSPPGFEAEPDEPKEEEIE

Parental  DPFVGVPPDYDFFGYGHGYGYPPPPPPEDPPQAPLA
          DPF.G.P.DYDFFG.GHGYGYPPP...EDPPQAP.A
Retrocopy DPFAGIPLDYDFFGFGHGYGYPPP---EDPPQAPFA

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_10 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA03G0415200	3 retrocopies	retro_ogla_10 , retro_ogla_71, retro_ogla_74,