RetrogeneDB ID: retro_oglu_15

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 1:31293515..31294547(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM01G31610
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM08G04830
• Aliases: None
• Description: None

Sequence

>retro_oglu_15
ATGAGGCGACCCATGGCTCGCGATTTTACGGCGACGTTTCTTCTGCTGCTCAGCGTCGCGTCGCTGCTGGTGATCTCGCC
GTGCGCGGCCCAGCAGATCAAGACCACCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCG
AGAGCCTCGCCTTCGACGGCAAGGACGGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGAGGCAGCGCC
GCCGGCTGGACCACGTTCGCGTACAATGCGAACTACCGGAAAATCCCTCTCTGCTCGTCGTCCGAGGTGCCACCGGAGGA
GAGGGAGAGCATCTGCGGGCGCCCGCTGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACA
AGGGGCTGATGAAGGTCGGGCCCGACGGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTC
CTCAATGGCCTTGACGTCGACCAAGCTACGGGTGATGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAA
CGGGGAGATCACGATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGA
AGGCCGACCTGCCGTACCCGAACGGCGTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGC
CAGGCGTTCCGGTACTGGCTGCGGGGCACCAAAGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAA
CGTGAGGCGCGACACCAAGGGAGGCTACTGGGTGGCGCTCAACCAGGAGAGGATGCGGTTGGGCGCGGCGCCCGCAGCCA
AGCACCTGGTCGGCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTGCCAAGGGCGTCACGCTCAGC
GAGGTGGCGGAGCAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATTGGCATGTTTGCTTGA

Alignment

ORF - retro_oglu_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 82.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGFPATLLVTLLRLVGCLLLVCLAAPPCAAQQVKTSHAQFAFHLPLPDGVTGAESLAFDSSNHGPYTGVS
          R.F.AT.L..LL..V..LL.......PCAAQQ.KT.......HLPLPDGV.GAESLAFD....G.YTGVS
Retrocopy RDFTATFL--LLLSVASLLVIS----PCAAQQIKTTDTRWSYHLPLPDGVSGAESLAFDGKD-GLYTGVS

Parental  DGRVLRWGGAAAGWTTFAHHQDYRKIPMCTTPVAPPEETESMCGRPLGLAFHDRTGDLYIADAYKGLMHV
          DGRVL.WGG.AAGWTTFA....YRKIP.C.....PPEE.ES.CGRPLG......TG.LYIADAYKGLM.V
Retrocopy DGRVLKWGGSAAGWTTFAYNANYRKIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADAYKGLMKV

Parental  GPRGGEAEVLAAGADGVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATSRLLKYDAATKQ
          GP.GGEA.V.A..ADGVPF.F.NG.DVDQATGD.YFTDSS.TY.RRFN.EI.MNADAT.RLLKYDA.T..
Retrocopy GPDGGEAQVVATEADGVPFHFLNGLDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRR

Parental  VTVLRSGLPYANGVAVSRDGSHAVVAHTVPCQAFRYWIKGPNAGEYELLADLPGYPDNVRRDARGGYWVA
          VTVL...LPY.NGVAVSRD..H.VVAHTVPCQAFRYW..G..AGEYEL.ADLPGYPDNVRRD..GGYWVA
Retrocopy VTVLKADLPYPNGVAVSRDRTHLVVAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRDTKGGYWVA

Parental  LNQEKVRLDATAAA
          LNQE..RL.A..AA
Retrocopy LNQERMRLGAAPAA

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_15 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15 ,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,