RetrogeneDB ID: retro_ogla_75

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 9:9575217..9575930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA05G0075600
• Aliases: None
• Description: None

Sequence

>retro_ogla_75
AGTTTGGTTGACATGTTTTCTACACAAGAGATTAGCAGCCACGTAAGCATCGTCCCAGCAGATAAAGCTCCTGGCCCAGA
TGGATTCAATGGCTATTTTCTGAATAAATGCTGGCACATTATAATCCAAGATTATTACGGACTAGCTGCACACTTCCATG
CTAGTTGTACTGATCTACAGATCCGTAATAGCTCTTACATAACTTTGGTCCCAAAGAAGAGTTCTCCAAAGACTGTCAAT
GATTTTAGACCTATTTCCCTCATGGGGCTCAGCCTAAAATTTCTTACCAAACTCATGGCAGATAGATTGCAAGGGGTAAT
TCTCAAGCTAGTCAGTGATAATTAGTATGGCTTTATCAAAGGAAGAACTATACAACACTGCCTTGCTTGGTCTTTTGAAT
ACATTCACCAGTGCCAACAGTCTAAGAGAGAGATCATACTCCTGAAATTGGACTTTGAAAAGGCTTTTGACACCATTGAG
CACTCTGCTATTCTCTCAGTCCTGAAGCATATGGGTTTTCCTGAAAAATGGATTCATTGGGTACAGATGGTCTTTTCCAT
ACCTCCTCTGTTGTTCTTCTTAATGGAGAGCCAGGGAATTCTTTCAAGTGTAAAAGAGGGGTGAGGCAAGGTGATCCTCT
GTCCCCTTTACTCTTTGTCTTAGGTGCTGAGCTTCTACAAAAAATAGTAAACAAAGCCTCTGATATGGGTTTG

Alignment

ORF - retro_ogla_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVISFYENPLLRSHLALAFVDKLEERRDLNLAEWNFRLFIKSKDFYNLCAQFCEGSLVLESINRSFITLV
          ............SH......DK.......N....N....I...D.Y.L.A.F......L...N.S.ITLV
Retrocopy SLVDMFSTQEISSHVSIVPADKAPGPDGFNGYFLNKCWHIIIQDYYGLAAHFHASCTDLQIRNSSYITLV

Parental  PKKSSPEKVNDFRPISLQSVALKLLTKVLADRLQSVIIELIHQNQYGFIKARNIQDCLAWSFEYLHQCQH
          PKKSSP..VNDFRPISL....LK.LTK..ADRLQ.VI..L...N.YGFIK.R.IQ.CLAWSFEY.HQCQ.
Retrocopy PKKSSPKTVNDFRPISLMGLSLKFLTKLMADRLQGVILKLVSDN*YGFIKGRTIQHCLAWSFEYIHQCQQ

Parental  SKREIVLLKLDFEKTFDTIEHSVILDIMRQKGFDSKWISWISQIFS-SASSSVILNGVLGKSFYCKRGVR
          SKREI.LLKLDFEK.FDTIEHS.IL......GF..KWI.W....FS...SS.V.LNG..G.SF.CKRGVR
Retrocopy SKREIILLKLDFEKAFDTIEHSAILSVLKHMGFPEKWIHWVQMVFS<HTSSVVLLNGEPGNSFKCKRGVR

Parental  QGDPLSPLLFVLGADLLQSIVNKACSQGV
          QGDPLSPLLFVLGA.LLQ.IVNKA...G.
Retrocopy QGDPLSPLLFVLGAELLQKIVNKASDMGL

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_75 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	ORGLA05G0075600	1 retrocopy	retro_ogla_75 ,