RetrogeneDB ID: retro_oglu_5

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 8:18663058..18664654(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM08G15930
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM09G09430
• Aliases: None
• Description: None

Sequence

>retro_oglu_5
ATGGCGGCGGCGACGACAATGTGCGCCGCGGTGGCGGTGCTCCTCGTTCTGACGTCGACAATGGCGGCCGCCGCCGGCGA
TGGCGATGGCGATGGCGGTGGCGGTGGCTTCGACTACAAGAAGGCGCTGCACAGCGGGCTGCTCTACTTCGAGGCGCAGC
GGTCGGGGCACCTGCCGTACAACCAGCGGGTGCGGTGGCGCGGCCACTCGGGGCTCGCCGACGGGCTGCAGCAAGGGGTG
GACCTCGTCGGCGGCTACTACGACGCCGGCGACAACGTGAAGTTCGGTCTGCCCATGGCGTTCACGATGACGATGCTGTC
GTGGGCCGCGGCGGAGTTCTGGGACGAGATCGCCGCCGCCGGCGAGCGGCGGCACGTGCTGGAGGCCATCAAGTGGGGCA
CCGACTACCTCGTGAAGGCGCACACCGCCGCCGACGAGCTGTGGGCCGAGGTCGGCGACGGCGACACCGACCACTACTGC
TGGCAGCGGCCGGAGGACATGACGACGTCGAGGCAGGCCTACAAGGTGGACCGCGACAACCCCGGCTCCGACGTCGCCGG
CGAGACCGCCGCCGCGCTCGCCGCCGCGTCCATCGTGTTCCGCCGCTCCAACCCCCGCTACTCCCGCCTCCTCCTCCGCC
ACGCCGAGCAGCTGTTCGACTTCGGCGACAGGTACAGGGGCAAGTACGACAGCAGCATCGGCGAGGTGAGGGCGTACTAC
GCGTCGGTGAGCGGCTACGGCGACGAGCTGCTGTGGGCGGCGCTGTGGCTGCACCGCGCCACCGGCCGCCGCGGCTACCT
CGACTACGCTGTCGCCATGGCCGACGAGCTCGGCGGCGTCGGCTGGGCCGTCACCGAGTTCAGCTGGGACGTCAAGTACG
CCGGCCTCCAGATCCTCGCCGCCAAGGTGCTCATGGACGGCGGCGACCACCCGGCGTCGCACGCGGCGACGCTGGAGCAG
TACAGGTCCAAGGCGGAGCACTACCTCTGCGCCTGCCTCGGCAAGAACGCCGCCGCCGGCGACAACGTCAACCGCACCGC
CGGCGGCATGCTGTTCGTCCGCCGCTGGAACAACATGCAGTACGTCACCAACGCCGCCTTCCTCCTCACCGTCTACTCCC
GCTACCTCCGTGACTCCGGCGGCGACACCATCCGGTGCTCCGGTGGGGCTATGGCAACCGGCGACGAGTTGGCGGCGATG
GCGAGGGCGCAGGCGGACTACGTGCTGGGCGACAACCCGGCGGGGGTGAGCTACATGGTCGGGTACGGGCGGCGGTTCCC
GCGGCGGGTGCACCACCGCGGGGCGTCCATGGTGTCGCACCGCGCGGACGGGCGGTTCGTGGGGTGCGTGCAGGGGTACG
ACCGCTGGTTCCGGCGCGGCGGCGCGAACCCGAACGTGGTCGCCGGAGCCATCGTCGGCGGGCCGGACCACCGCGACAGG
TTCAGGGACAGCCGCGACAACTACATGCAGACGGAGGCGTGCACGTACAACACCGCGCCCATGGTCGGCGTCTTCGCGCA
CCTGCACGCCCAGAAGATGGCGGCGAGGACTGCTAATAATAATGCCGATCGATCGATGATTAAACGAGTGGATTGA

Alignment

ORF - retro_oglu_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 81.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTLAAVLVLFLLAVVTLPLRCDAASAGGEEEEEQQPLDYREALEKSLLYFEAQRSGRLPYSQRVTWRGHS
          TT..A.....L....T......AA...G.........DY..AL...LLYFEAQRSG.LPY.QRV.WRGHS
Retrocopy TTMCAAVAVLLVLTSTMA----AAAGDGDGDGGGGGFDYKKALHSGLLYFEAQRSGHLPYNQRVRWRGHS

Parental  GLTDGLQQGVDLVGGYYDAGDHVKFGLPMAFTVTMLSWGAIDFAADIAAAGEWRHALEAIKWGTDYFVKA
          GL.DGLQQGVDLVGGYYDAGD.VKFGLPMAFT.TMLSW.A..F...IAAAGE.RH.LEAIKWGTDY.VKA
Retrocopy GLADGLQQGVDLVGGYYDAGDNVKFGLPMAFTMTMLSWAAAEFWDEIAAAGERRHVLEAIKWGTDYLVKA

Parental  HTHPFVYWAEVGDGDTDHYCWQRPEDMTTSRQAYRVDRDNPGSDLAGETAAALAAASIVFRRSDPHYSHL
          HT.....WAEVGDGDTDHYCWQRPEDMTTSRQAY.VDRDNPGSD.AGETAAALAAASIVFRRS.P.YS.L
Retrocopy HTAADELWAEVGDGDTDHYCWQRPEDMTTSRQAYKVDRDNPGSDVAGETAAALAAASIVFRRSNPRYSRL

Parental  LLHHAQQLFEFGDTYRGSYDSSIEEVRSYYASVSGYHDELLWAALWLHRATGKEEYLRYAVDNADSFGGV
          LL.HA.QLF.FGD.YRG.YDSSI.EVR.YYASVSGY.DELLWAALWLHRATG...YL.YAV..AD..GGV
Retrocopy LLRHAEQLFDFGDRYRGKYDSSIGEVRAYYASVSGYGDELLWAALWLHRATGRRGYLDYAVAMADELGGV

Parental  GWAITEFSWDVKYAGLQVLAAKLLLDGDPQAAAHRGVLEKYREKAEHYLCACLGRNTNGADNVDRSPGGM
          GWA.TEFSWDVKYAGLQ.LAAK.L.DG....A.H...LE.YR.KAEHYLCACLG.N....DNV.R..GGM
Retrocopy GWAVTEFSWDVKYAGLQILAAKVLMDGGDHPASHAATLEQYRSKAEHYLCACLGKNAAAGDNVNRTAGGM

Parental  LYVRQWNNLQYASSAAFLLTAYSHYLSSSSASASAALRCPGGAAAAA-EMVSLARSQADYILGRNPLRLS
          L.VR.WNN.QY...AAFLLT.YS.YL..S........RC.GGA.A...E....AR.QADY.LG.NP...S
Retrocopy LFVRRWNNMQYVTNAAFLLTVYSRYLRDSGGD---TIRCSGGAMATGDELAAMARAQADYVLGDNPAGVS

Parental  YMVGYGRRYPARVHHRGASIVSHKEDGRFIGCVQGFDDWFGRGRANPNVLAGAIVGGPSRRDEFRDDRAN
          YMVGYGRR.P.RVHHRGAS.VSH..DGRF.GCVQG.D.WF.RG.ANPNV.AGAIVGGP..RD.FRD.R.N
Retrocopy YMVGYGRRFPRRVHHRGASMVSHRADGRFVGCVQGYDRWFRRGGANPNVVAGAIVGGPDHRDRFRDSRDN

Parental  YMQTEACTYNTAPMVAVFARLHRLTTAITTA
          YMQTEACTYNTAPMV.VFA.LH....A..TA
Retrocopy YMQTEACTYNTAPMVGVFAHLHAQKMAARTA

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_5 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM09G09430	1 retrocopy	retro_oglu_5 ,
Oryza nivara	ONIVA09G08070	1 retrocopy	retro_oniv_5,