RetrogeneDB ID: retro_ogla_31

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 12:1542459..1543557(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA12G0020700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA11G0022300
• Aliases: None
• Description: None

Sequence

>retro_ogla_31
ATGGCGGAAGAAGATGACAAGAAGCAGAAGGGCCCCGATGTGACGGTGCCCTCGGGATACTTCTTCGTGCCGAAGCCGGA
GCAGCTCATCCGCGACTACCTCAACCACTGGATCACCGGCCGGCCGATCGAGGAGCTCCGGGACATCGTCCGGGAAGCCG
ACGTCTACGGCTCCGACCCGGCGACGCTGACGGAGGCGCACAGGGCGTACGGCCACGACGGCAAGTCGTGGTACTTCCTC
ACCGTCGCCAAGTGGAAGGGCGGCAGGGGCGGCGCCGGCACCGCCGGCCGGCTCAACCGCTGCGTCGAGGGCGGCGGCAC
GTGGCACAACTCGCAGCGCCGCCGCGTCATCGAGGGCTACGGCGACCGCCAGGCGTTCGAGTACCGCGCCCCCGGGAACA
AGAAGACGGACTGGCTCATGGAGGAGATCGCCAGCAACCTGCCGGCGGCGATCACCGACGAGGGCATCATGGTCATCTGC
AAGGTCTACCTCTCGCCGAGGGCCAAGCAGGCGACGGCCGACGAGGAGGAACGCCAAGAAACCAACGTGGTTCCCGGGCC
CAAGAGGCTCCGAGAGGCGGAAGCCACCGGCTACGACGCGCCGGCGCCGGAGACGCCACAGCCCGACGTCGGATGCTCGT
ACTCCGGCGGCGGCGAGACGTCTCAAGCGACCGCCTCGATGGACTACTGCTGCTCGACGACGACACACACGGCGGACGAC
ACGGCCAATGCCGCCGCCTACTACTACGGCGACGTTGATGCCATCAAGCCAGATGCTTACGACGGCGGCGACTACGGCAT
CGGCATCAACGCAGACGGGGAGCTGGTTCTCTGCGGCAACGGCCACGGTGGCATCGGGACGCAGGGACAGATGCCATTGG
CAATGCAGAACACCAACGGGGAGATGACCTTGTTCTCACCGATGAACGGCTATGGTGTTGGCTTCAATGAGGAGGTGAGA
CAAGAACCACAAGTAGGAGGTGAGGTGGAGATGAATGATTTCTTCAACGATTTGTTCGTCGACTTCGACGGCGCCGGTGA
TCCCAATCCCAATCCCAACGAGGGTGGAGACAGCCACGGCCACATACTATGTGAATGA

Alignment

ORF - retro_ogla_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 65.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEDDKKQKGPDVTVPSGYFFVPKPEQIIRDYLNHWITGRPIEELRDIVREADVYGSDPATLTEEHSAY
          MAEEDDKKQKGPDVTVPSGYFFVPKPEQ.IRDYLNHWITGRPIEELRDIVREADVYGSDPATLTE.H.AY
Retrocopy MAEEDDKKQKGPDVTVPSGYFFVPKPEQLIRDYLNHWITGRPIEELRDIVREADVYGSDPATLTEAHRAY

Parental  GHDGKSWYFLTVAKWKGGRGGAGTAGRINRCVEGGGTWHNSQRRRVIEGYGDRQAFEYRAPGNKKTDWLM
          GHDGKSWYFLTVAKWKGGRGGAGTAGR.NRCVEGGGTWHNSQRRRVIEGYGDRQAFEYRAPGNKKTDWLM
Retrocopy GHDGKSWYFLTVAKWKGGRGGAGTAGRLNRCVEGGGTWHNSQRRRVIEGYGDRQAFEYRAPGNKKTDWLM

Parental  EEIASNLPAAITDEGIMVICKVYLSPRAKEATADDEERQETNVVPGPKRLREAEATGYDAPAP--PQPDV
          EEIASNLPAAITDEGIMVICKVYLSPRAK.ATAD.EERQETNVVPGPKRLREAEATGYDAPAP..PQPDV
Retrocopy EEIASNLPAAITDEGIMVICKVYLSPRAKQATADEEERQETNVVPGPKRLREAEATGYDAPAPETPQPDV

Parental  GCSYSDGSETSQATASMDYFAARRRHTRRTT
          GCSYS.G.ETSQATASMDY......HT...T
Retrocopy GCSYSGGGETSQATASMDYCCSTTTHTADDT

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_31 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	ORGLA11G0022300	1 retrocopy	retro_ogla_31 ,