RetrogeneDB ID: retro_ogla_42

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: Oglab07_unplaced150:336176..336632(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA07G0251100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA08G0005800
• Aliases: None
• Description: None

Sequence

>retro_ogla_42
ATGGGCCGCATGCACAGCAGCGGGAAGGGGATGTCCTGCTCGGTGCTCCCCTACAGGCGCGCCGCTCCCGCCTGGGTCAA
GACGTCCGCGTCGGAGGTGGAGGAGATGATCGTGCGCGCCGCCAAGAAGGGCCAGCTGCCGTCGCAGATCGGGGCGATCC
TCCGCGACGCCCACGCCGTCCCGCTCGCCCAGGGCGTCACCGGCGGCAAGATCCTCCGCGTGCTCAAGTCCCGCGGCCTC
GCGCCCGAGGTGCCCGAGGACCTCTACTTCCTCATCAAGAAGGCCGTCGCGATGAGGAAGCACCTCGAGAGGAACAGGAA
GGACAAGGACACCAAGTTCCGCCTCATCCTCGTCGAGAGCAGGGTGCACCGCCTCACCCGCTACTACCGCCTCGCCAAGA
AGATCCCCGCCTTATTCAAGTACGACTCCACCACCGCGAGCACTCTCGTGGCCTGA

Alignment

ORF - retro_ogla_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHSRGKGISSSAIPYKRTPPSWVKTAAADVEEMIMKAAKKGQMPSQIGVVLRDQHGIPLVKSVTGSK
          MGRMHS.GKG.S.S..PY.R..P.WVKT.A..VEEMI..AAKKGQ.PSQIG..LRD.H..PL...VTG.K
Retrocopy MGRMHSSGKGMSCSVLPYRRAAPAWVKTSASEVEEMIVRAAKKGQLPSQIGAILRDAHAVPLAQGVTGGK

Parental  ILRILKAHGLAPEIPEDLYFLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWK
          ILR.LK..GLAPE.PEDLYFLIKKAVA.RKHLERNRKDKD.KFRLILVESR.HRL.RYY...KK.P...K
Retrocopy ILRVLKSRGLAPEVPEDLYFLIKKAVAMRKHLERNRKDKDTKFRLILVESRVHRLTRYYRLAKKIPALFK

Parental  YESTTASTLVA
          Y.STTASTLVA
Retrocopy YDSTTASTLVA

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_42 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB02G23100	1 retrocopy	retro_obra_7,
Oryza punctata	OPUNC08G01190	1 retrocopy	retro_opun_35,
Oryza glaberrima	ORGLA08G0005800	1 retrocopy	retro_ogla_42 ,
Sorghum bicolor	Sb07g001620	1 retrocopy	retro_sbic_47,