RetrogeneDB ID: retro_oniv_5

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 8:17919417..17921007(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA08G16330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA09G08070
• Aliases: None
• Description: None

Sequence

>retro_oniv_5
ATGGCGGCGGCGATGACAATGTGCGCCGCGGTGGCGGTGCTCCTCGTTCTGACGTCGACAATGGCGGCCGCCGCCGGCGA
TGGCGATGGCGATGGCGGTGGCTTCGACTACAAGAAGGCGCTGCACAGCGGGCTGCTCTACTTCGAGGCGCAGCGGTCGG
GGCACCTGCCGTACAACCAGCGGGTGCGGTGGCGCGGCCACTCGGGGCTCGCCGACGGGCTGCAGCAAGGGGTGGACCTC
GTCGGCGGCTACTACGACGCCGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGATGACGATGCTGTCGTGGGC
CGCGGCGGAGTTCTGGGACGAGATCGCCGCCGCCGGCGAGCGGCGGCACGTGCTGGAGGCCATCAAGTGGGGCACCGACT
ACCTCGTGAAGGCGCACACCGCCGCCGACGAGCTGTGGGCCGAGGTCGGCGACGGCGACACCGACCACTACTGCTGGCAG
CGGCCGGAGGACATGACGACGTCGAGGCAAGCCTACAAGGTGGACCGCGACAACCCCGGCTCCGACGTCGCCGGCGAGAC
CGCCGCCGCGCTCGCCGCCGCGTCCATCGTGTTCCGCCGCTCCAACCCCCGCTACTCCCGCCTCCTCCTCCGCCACGCCG
AGCAGCTGTTCGACTTCGGCGACAGGTACAGGGGCAAGTACGACAGCAGCATCGGCGAGGTGAGGGCGTACTACGCGTCG
GTGAGCGGCTACGGCGACGAGCTGCTGTGGGCGGCGCTGTGGCTGCACCGCGCCACCGGCCACCGCGGCTACCTCGACTA
CGCCGTCGCCATGGCCGACGAGCTCGGCGGCGTCGGCTGGGCCGTCACCGAGTTCAGCTGGGACGTCAAGTACGCCGGCC
TCCAGATCCTCGCCGCCAAGGTGCTCATGGACGGCGGCGACCACCCGGCGGCGCACGCGGCGACGCTGGAGCAGTACAGG
TCCAAGGCGGAGCACTACCTCTGCGCCTGCCTCGGCAAGAACGCCGCCGCCGGCGACAACGTCAACCGCACCGCCGGCGG
CATGCTGTTCGTCCGCCGCTGGAACAACATGCAGTACGTCACCAACGCCGCCTTCCTCCTCACCGTCTACTCCCGCTACC
TCCGCGACTCCGGCGGCGACACCATCCGGTGCTCCGGTGGGGCTATGGCAACCGGCGACGAGTTGGCGGCGATGGCGAGG
GCGCAGGCGGACTACGTGCTGGGCGACAACCCGGCGGGGGTGAGCTACATGGTCGGGTACGGGCGGCGGTTCCCGCGGCG
GGTGCACCACCGCGGGGCGTCCATGGTGTCGCACCGCGCGGACGGGCGGTTCGTGGGGTGCGTGCAGGGGTACGACCGCT
GGTTCCGGCGCGGCGGCGCGAACCCGAACGTGGTCGCCGGAGCCATCGTCGGCGGGCCGGACGACCGCGACAGGTTCAGG
GACAGCCGCGACAACTACATGCAGACGGAGGCGTGCACGTACAACACCGCGCCCATGGTCGGCGTCTTCGCGCACCTGCA
CGCCCAGAAGATGGCGGCGAGGACTGCTAATAATAATGCCGATCGATCGATGATTAAACGAGTGGATTGA

Alignment

ORF - retro_oniv_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.52 %
• Parental protein coverage: 93.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAAVLVLVLLAVVALPLRCDAVSAGGEEEEEQQPLDYREALEKSLLYFEAQRSGRLPYSQRVTWRGHSGL
          .AA.........V.L.L......A.G.........DY..AL...LLYFEAQRSG.LPY.QRV.WRGHSGL
Retrocopy MAAAMTMCAAVAVLLVLTSTMAAAAGDGDGDGGGFDYKKALHSGLLYFEAQRSGHLPYNQRVRWRGHSGL

Parental  TDGLQQGVDLVGGYYDAGDHVKFGLPMAFTVTMLSWGAIDFAADIAAAGEWRHALEAIKWGTDYFVKAHT
          .DGLQQGVDLVGGYYDAGD.VKFGLPMAFT.TMLSW.A..F...IAAAGE.RH.LEAIKWGTDY.VKAHT
Retrocopy ADGLQQGVDLVGGYYDAGDNVKFGLPMAFTMTMLSWAAAEFWDEIAAAGERRHVLEAIKWGTDYLVKAHT

Parental  HPFVYWAEVGDGDTDHYCWQRPEDMTTSRQAYRVDRDNPGSDLAGETAAALAAASIVFRRSDPHYSHLLL
          .....WAEVGDGDTDHYCWQRPEDMTTSRQAY.VDRDNPGSD.AGETAAALAAASIVFRRS.P.YS.LLL
Retrocopy AADELWAEVGDGDTDHYCWQRPEDMTTSRQAYKVDRDNPGSDVAGETAAALAAASIVFRRSNPRYSRLLL

Parental  HHAQQLFEFGDTYRGSYDSSIEEVRSYYASVSGYHDELLWAALWLHRATGKEEYLRYAVDNADSFGGVGW
          .HA.QLF.FGD.YRG.YDSSI.EVR.YYASVSGY.DELLWAALWLHRATG...YL.YAV..AD..GGVGW
Retrocopy RHAEQLFDFGDRYRGKYDSSIGEVRAYYASVSGYGDELLWAALWLHRATGHRGYLDYAVAMADELGGVGW

Parental  AITEFSWDVKYAGLQVLAAKLLLDGDPQAAAHRGVLEKYREKAEHYLCACLGRNINGADNVDRSPGGMLY
          A.TEFSWDVKYAGLQ.LAAK.L.DG....AAH...LE.YR.KAEHYLCACLG.N....DNV.R..GGML.
Retrocopy AVTEFSWDVKYAGLQILAAKVLMDGGDHPAAHAATLEQYRSKAEHYLCACLGKNAAAGDNVNRTAGGMLF

Parental  VRQWNNLQYASSAAFLLTAYSHYLSSSSASASAALRCPSGAAAAA-EMVSLARSQADYILGRNPLRLSYM
          VR.WNN.QY...AAFLLT.YS.YL..S........RC..GA.A...E....AR.QADY.LG.NP...SYM
Retrocopy VRRWNNMQYVTNAAFLLTVYSRYLRDSGGD---TIRCSGGAMATGDELAAMARAQADYVLGDNPAGVSYM

Parental  VGYGRRYPARVHHRGASIVSHKEDGRFIGCVQGFDDWFGRGRANPNVLAGAIVGGPSRRDEFRDDRANYM
          VGYGRR.P.RVHHRGAS.VSH..DGRF.GCVQG.D.WF.RG.ANPNV.AGAIVGGP..RD.FRD.R.NYM
Retrocopy VGYGRRFPRRVHHRGASMVSHRADGRFVGCVQGYDRWFRRGGANPNVVAGAIVGGPDDRDRFRDSRDNYM

Parental  QTEACTYNTAPMVAVFARLHRLTTAITTA
          QTEACTYNTAPMV.VFA.LH....A..TA
Retrocopy QTEACTYNTAPMVGVFAHLHAQKMAARTA

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_5 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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.

---

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 ,