RetrogeneDB ID: retro_ogla_74

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 9:2695494..2695899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ogla_74
GGGCCTGTGCCTCGAGACATCCCCTCCACATCCTCTCAGCCGCCTTTTGCTCCTGAGCGTCCTTCCTCTATGGCTCGTCG
TGAGCCATCTCCCTTATTTCGCATTTTGCGGACTCTTTTTGGCCTTTGCTCCGTGGAGGCTAAAAAGAACCGCCGATTGC
GGAATTTGGCGAAGAAAACGGCTCGTGATGTCAAGTACCTCAAGGCGAGGTATCACGAGGACCACCACATTGATATCCCT
CCTTCCCCTCCGGGTTTCGAGGCCGAACTCGATGAGCCCGAGGAGGAAGAGATAGAGGATCCATTTGTTGGGGTGCCTCC
TGATTATGATTTCTTTGGTTATGGCCATGGCTATGGCTATCCCCCTCCGCCTCCTCCAGAGGATCCTCCTCAGGCGCCCC
TTGCT

Alignment

ORF - retro_ogla_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 76.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPQVANVPRGSSLPPESAERPSSMARREPSPLFRILRTLFGLCSVEAKKNRRLRNLAKKTARDVKYLKAR
          GP.....P..SS.PP...ERPSSMARREPSPLFRILRTLFGLCSVEAKKNRRLRNLAKKTARDVKYLKAR
Retrocopy GPVPRDIPSTSSQPPFAPERPSSMARREPSPLFRILRTLFGLCSVEAKKNRRLRNLAKKTARDVKYLKAR

Parental  YHEDHHIDIPPSPPGFEAELDEPEEEEIEDPFVGVPPDYDFFGYGHGYGYPPPPPPEDPPQAPLA
          YHEDHHIDIPPSPPGFEAELDEPEEEEIEDPFVGVPPDYDFFGYGHGYGYPPPPPPEDPPQAPLA
Retrocopy YHEDHHIDIPPSPPGFEAELDEPEEEEIEDPFVGVPPDYDFFGYGHGYGYPPPPPPEDPPQAPLA

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_74 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 ,