RetrogeneDB ID: retro_ogla_64

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 4:23674131..23674446(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA05G0188400
• Aliases: None
• Description: None

Sequence

>retro_ogla_64
TTCGACGCGTTCGCGGACGCGCAGGGGGAGGACGCCGCCGCCGGCCGCGGCGCCGGTGGCGACTACGTGCACGTCCGCGT
GCAGCAGCGCAATGGGCGGAAGACGCTGACCACCGTGCAGGGGATCGGCGGCGAGTACAACTACGCCAAGGTGCTCCGCG
ACCTCAAGCGGGAGCTCTGCTGCAACGGCAACGTGGTGGAGGACAAGGAGCTCGGCAAGATCATCCAGCTGCAGGGCGAC
CACCGCAACAGCGTCTCCGACTTCCTCGCCAAGGCCGGCATGGTCCGCAAGGACAACATCAAGGTCCACGGATTC

Alignment

ORF - retro_ogla_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 90.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDPFAEANAEDSGAGPGAK-DYVHVRIQQRNGRKSLTTVQGLKKEYSYNKILKDLKKEFCCNGTVVQDPE
          FD.FA.A..ED..AG.GA..DYVHVR.QQRNGRK.LTTVQG...EY.Y.K.L.DLK.E.CCNG.VV.D.E
Retrocopy FDAFADAQGEDAAAGRGAGGDYVHVRVQQRNGRKTLTTVQGIGGEYNYAKVLRDLKRELCCNGNVVEDKE

Parental  LGQVIQLQGDQRKNVATFLVQAGIAKKDNIKIHGF
          LG..IQLQGD.R..V..FL..AG...KDNIK.HGF
Retrocopy LGKIIQLQGDHRNSVSDFLAKAGMVRKDNIKVHGF

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_64 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	ORGLA05G0188400	1 retrocopy	retro_ogla_64 ,