RetrogeneDB ID: retro_oglu_12

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 1:44985465..44986194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM01G48230
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM01G48220
• Aliases: None
• Description: None

Sequence

>retro_oglu_12
ATGGCGTCGCCGGCGCCGGCGCCGAAGCCGGCGCCGGTGAAGGTGATCGGCACCTTCGACAGCCCGTACAGCCACCGCGC
GGAGGCCGCCCTGCGGCTCAAGGGCGTGCCATACGAGCTCATCCTGGAGGACCTCCGCAACAAGAGCGACCTGCTGCTCA
CCCACAACCCCATCCACAAGAAGGTCCCCGTCCTCCTCCACGGCGACGACGACCACCGCGCCGCCGTCTGCGAGTCCCTC
GTCGTCGTCGAGTACGTCGACGAGGCGTTCCCCGGCCCGCCCTTCCTCCTCCCCGCCGACCCCGGCCTCCGCGCCGCCGC
CCGCTTCTGGGCCCGGTTCATCGACGACAAGTGCACGAAGCCGTTCTGGCTGGCGCTGTGGTCGACGGACGACGGCGAGG
TGCGGGAGGGCTTCGCGGCGGAGATCAAGGAGAACCTGAAGCTCCTCGAGGCGCAGCTCAAGGGGAGGCGATTCTTCGGA
GGCGACGCCATCGGCTACCTCGACCTGGCCGCCAGTGGGTACGCCTACTGGCTGGAGGTGCTCGAGGAGGTCGCCGGGGT
GAGCCTGGTCACCGCCGACGAGTTCCCCGACCTCTGCCGCTGGGCGAAGGAGTACGCCGCCGACGACAGGATCAAGGCGT
GCCTCCCGGACAGGGCCAAGCTGCTCGAACACTTCACGGCGATGAAGGAGATGTTCATGGCGACGGCGAGGTCAATGGCG
GCAAAATGA

Alignment

ORF - retro_oglu_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 97.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKLIGAFASAYGHRAEAALRLKGVQYELLLEDLRSKSDLLLAHNPVHKLVPVLLHSDG---RSVAESLVV
          VK.IG.F.S.Y.HRAEAALRLKGV.YEL.LEDLR.KSDLLL.HNP.HK.VPVLLH.D......V.ESLVV
Retrocopy VKVIGTFDSPYSHRAEAALRLKGVPYELILEDLRNKSDLLLTHNPIHKKVPVLLHGDDDHRAAVCESLVV

Parental  VQYVDDAFHGPP-LLPADPYARAQARFWAQFIDDKFSRPFWLSFWM-EDGEKKEAFVREAKENLRPLEAQ
          V.YVD.AF.GPP.LLPADP..RA.ARFWA.FIDDK...PFWL..W...DGE..E.F..E.KENL..LEAQ
Retrocopy VEYVDEAFPGPPFLLPADPGLRAAARFWARFIDDKCTKPFWLALWSTDDGEVREGFAAEIKENLKLLEAQ

Parental  LDGGNKRFFGGDAIGLVDIAASGLAHWVGVFEEVTGVSLVSEREFPALCRWSQRYVNDGAVRQCLPSRDE
          L.G...RFFGGDAIG..D.AASG.A.W..V.EEV.GVSLV...EFP.LCRW...Y..D.....CLP.R..
Retrocopy LKG--RRFFGGDAIGYLDLAASGYAYWLEVLEEVAGVSLVTADEFPDLCRWAKEYAADDRIKACLPDRAK

Parental  LVALFTANKEAYTLLAKA
          L...FTA.KE.....A..
Retrocopy LLEHFTAMKEMFMATARS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza glumaepatula was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_12 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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 glumaepatula	OGLUM01G48220	1 retrocopy	retro_oglu_12 ,