RetrogeneDB ID: retro_ogla_37

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 3:32614552..32615296(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA03G0385900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA03G0005200
• Aliases: None
• Description: None

Sequence

>retro_ogla_37
ATGATGATGGAGAATAGCAGGGAGCAGCAGCCGGAGTCGTCGCCGGCGAACAACAATAGCAAGAAGAAGAAGAACAAGAA
GAAGACGGCGTCGCGGTTCCGGCGTGTGTGCGTGTTCTGCGGCAGCAGCCCCGGGAAGAAGGCGTCGTACCAGGTGGCCG
CCGTGCAGCTGGGGCAGCAGCTGGTGGAGCGCGGCATCGACCTGGTGTACGGCGGCGGCAGCGTTGGGCTGATGGGGCTG
GTGTCCCGCGCCGTCCACGGAGGCGGCGGGCACGTGGTGGGCGTGGTGCCCAATGGCGTGCTGCCACGCGAGCTGATCGG
CGAGACGCTGGGGGAGGTGAGGGCGGTGGGAAGCATGCACCAGCGGAAGGCGGAGATGGCGCGGGAGTCGGACGCCTTCA
TCGCCCTCCCCGGCGGCTACGGCACGCTGGAGGAGCTCCTGGAGGTCATCACCTGGGCTCAGCTCCGCATCCACCACAAG
CCCGTCGGCCTCCTCAACGTCGACGGCTACTACGACTCCCTGCTCGCCTTCATCGACAAGGCCGTCCACGAAGGCTTCGT
CTCGCCGCCCGCCCGCCGCATCATCGTCGCCGCGCCCACCGCCTCCGACCTGCTCTGCAAGCTCGAGGAATACGTGCCGC
CGCCGCACGACGCCACCGCCCTGAAGCTCACCTGGGAGATGTCCACCGTATCGGAGCAGCACGCCGGAAGCATCTACTCC
CCCAAGCCCGACATGGCACGCTAG

Alignment

ORF - retro_ogla_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.39 %
• Parental protein coverage: 97.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQQQQQQQQESRFKRTCVFCGSSQGNKTTYRDAAVDLAKELVARGIDLVYGGGSIGLMGLVSQAVYDGGR
          ..........SRF.R.CVFCGSS.G.K..Y..AAV.L...LV.RGIDLVYGGGS.GLMGLVS.AV..GG.
Retrocopy KKKKNKKKTASRFRRVCVFCGSSPGKKASYQVAAVQLGQQLVERGIDLVYGGGSVGLMGLVSRAVHGGGG

Parental  HVIGVIPKTLMTPEIIGETVGEVRPVSDMHQRKAEMARQSDAFIALPGGYGTLEELLEVITWAQLGIHHK
          HV.GV.P......E.IGET.GEVR.V..MHQRKAEMAR.SDAFIALPGGYGTLEELLEVITWAQL.IHHK
Retrocopy HVVGVVPNGVLPRELIGETLGEVRAVGSMHQRKAEMARESDAFIALPGGYGTLEELLEVITWAQLRIHHK

Parental  PVGLLNVDGYYNSLLTFIDQAVEEGFISPSARRIIVSAPTAQELMDKLEEYV-PYHDRVASGLNWE
          PVGLLNVDGYY.SLL.FID.AV.EGF.SP.ARRIIV.APTA..L..KLEEYV.P.HD..A..L.WE
Retrocopy PVGLLNVDGYYDSLLAFIDKAVHEGFVSPPARRIIVAAPTASDLLCKLEEYVPPPHDATALKLTWE

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_37 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA03G0005200	1 retrocopy	retro_ogla_37 ,
Oryza sativa japonica	OS03G0109300	1 retrocopy	retro_osat_14,