RetrogeneDB ID: retro_ogla_71

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 8:2087872..2088278(-)
• Located in intron of: ORGLA08G0025400

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_71
CAAGCAGGCTCCTCAGTAGCTAGGGACATCCCCTCCTCTTCCACTCAGCTGCCTTCTGCTCCTGAGCGCCCTTCATCTGT
GGCTCGTCATGAGCCGCCTCCCTTATCCCGCATTTTGCGGAGTCTTTTTGGTCTTTGCTCCGCGAAAGCCAAAAAGAACC
GCCGATTGCGGAATGCGGCGAAGAAAACGGCTCGCGACGTCAAGTACCTCAAGGCGCGGTATCATGAGGATCACCACATC
GATGTCCCTCCTTCCCCTCCGGGTTTTGAGGCCGAGCCCGATGAGCCCGAGGAGGAAGCGATCGAGGATCCGTTTGCTGG
GTTGCCTCCTGACTTCGATTTCTTTGGTTATGGCCATGATCTATGGCTATCCTCCTCCAGAGGATCCTCCTCAGGCACCC
TTTGCT

Alignment

ORF - retro_ogla_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETGPQVA-NVPRGSSLPPESAERPSSMARREPSPLFRILRTLFGLCSVEAKKNRRLRNLAKKTARDVKYL
          ..G..VA...P..S...P...ERPSS.AR.EP.PL.RILR.LFGLCS..AKKNRRLRN.AKKTARDVKYL
Retrocopy QAGSSVARDIPSSSTQLPSAPERPSSVARHEPPPLSRILRSLFGLCSAKAKKNRRLRNAAKKTARDVKYL

Parental  KARYHEDHHIDIPPSPPGFEAELDEPEEEEIEDPFVGVPPDYDFFGYGHG-YGYPPPPPPEDPPQAPLA
          KARYHEDHHID.PPSPPGFEAE.DEPEEE.IEDPF.G.PPD.DFFGYGH..YGYPPP...EDPPQAP.A
Retrocopy KARYHEDHHIDVPPSPPGFEAEPDEPEEEAIEDPFAGLPPDFDFFGYGHD>YGYPPP---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_71 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,