RetrogeneDB ID: retro_ogla_66

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 6:2688315..2688710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA11G0115300
• Aliases: None
• Description: None

Sequence

>retro_ogla_66
ATGGCCGAGGCGGAGCTCCCGCAGCAGGAGGTCAAGCTCTTCAGCCGCTGGTCCTTCGAGGACGTCCAGGTGAAGGACAT
GTCGCTGGCGGACTACCTGGCGGTGAACTCGACGAAGCACGCGGCGTACCTGCCGCACACGGCGGGGAGCAGGTACTCGG
CGAAGAGGTTCCGGAAGAAGGCGCAGTGCCCCATCGTGGAGCTCCTGATGACCAACTCGCTCATGATGCTACGGCCGCAA
CAACGACGGGAAGAATTATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAAC
CCCGTACAGGCCATTGTCGACGCCATCATCAACAGCGGCCCTCGTGATCAGGATGCGACCCGTATTGGGTCGAGC

Alignment

ORF - retro_ogla_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 63.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEVELPQQEVKLFSRWSFVDVQVNDISLVDYLAVNPTKHATYLPHTAG-RYSAKRFR-KAQCPIVERL-
          MAE.ELPQQEVKLFSRWSF.DVQV.D.SL.DYLAVN.TKHA.YLPHTAG.RYSAKRFR.KAQCPIVE.L.
Retrocopy MAEAELPQQEVKLFSRWSFEDVQVKDMSLADYLAVNSTKHAAYLPHTAGSRYSAKRFRKKAQCPIVELLM

Parental  TNSLMM-HGRNN-GKK-IMAVRIVKHAMEIIHLLTDANPIQVIVDAIINSGPR-EDATRIGSA
          TNSLMM..GRNN.GK..IMAVRIVKHAMEIIHLLTDANP.Q.IVDAIINSGPR..DATRIGS.
Retrocopy TNSLMM>YGRNNDGKN>IMAVRIVKHAMEIIHLLTDANPVQAIVDAIINSGPRDQDATRIGSS

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_66 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA11G0115300	1 retrocopy	retro_ogla_66 ,