RetrogeneDB ID: retro_oind_74

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 11:12174372..12176085(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA009088
• Aliases: None
• Description: None

Sequence

>retro_oind_74
CTGCTGGAAAGCATTCTCCAGTTCCTCACAACGGCACGTGATAGGAACATGGCATCGCTAGTCTGTCGCTACTGGTACCA
TGCTGAGGCGGAGACACGGCAAGAGCTCTTCATCAGAAACTGTTATGCTGTTTCTCCGAATCGTGTCATTGAGCGTTTTC
GTGGCCTGCGCTCCATCACTCTGAAGGGCAGGCCATGCTTCGCAGACTCCACTTTAGTGCCCAAAGGCTGGGGTGGATAC
GCATCGCCCTGGGTGGCTGCTTTGGGTCCCGCATACCCGCACCTTAAGTGCATCTTCCTCAAGCGGATGACGGTATCAGA
CAATGACCTCAGGCTCATCGCACAGTCATTCCCTCAGTTAAGGGAGCTCTCACTGATGAGCTGCGACAAGTTCAGTGCCA
CCGGCCTCGCCATAATTGCGGAGCAGTGCAGGCATCTCCATGTGCTTGATCTGATTAATGATAAAGTCGAGGACACAGTG
GACGAGCAGGTGGACTGGATCTCTATGTTTCCCAAGCCCAGCACGTCGCTGGAGTCTCTTCTGTTCAGCTGTGTTGACAC
GCCCTGCAACTTTGAGTCACTGGAGGCCCTTGTCGCGCGCTCACCAGGTCTGTGCCAGCTGGGTGTGAATCGCCATGTGA
CGGTAGAGCAGCTGTGCTGCCTCATGGCAATCGCTCCCAATCTAACGCACCTTGGCACGGGTGTGTTCCGGTCCAAGACT
GGCTACCCTGCAGGTGAGGCCCCTCCATCGGTGTCTGAACTTGCGACATACTTCGCAGCATGCAGGTCACTCCACTCTCT
CTCAGGTCTCCAGGACGCCAATCCAGATTACCTCCCTGCGATCTACCCGGTTTGTGCCAATCTCACATCCCTCAACATCA
GCTCTGCCACCTTAACAGGGCAACAGCTTGCTCCCATCATTCGCTCCTGTGGCAATCTCCGGACATTCTGTGTGCGTGAC
TCCATAGGTGATGATGGCCTTTCTGCCATCGCTGAGACGTGCTTAGATCTCCAGGATTTACGAGTGTATCGTTTGCTTCG
TGGGAGTGAGCATCATCTCTCAGTATCAGATGTTGGGCTTGAAACTATCTCGAAAGGCTGCCAAAAGCTTAAAACCCTAA
CATACTATTGTGGAAGCATGACAAATGCAGCAATGGTCATTATGTCCAGCAACTGCCCTAATCTTGAGGTCTTTCGCCTC
AACATTTTGAAAACTTATCTCCCTGATCGGATCACCGGGGAGCCAATGGATGAAGGTTTTGGAGCAATTGTGATGAATTG
CAAGAAGCTTTCCAGGCTTTCGACCTCTGGTCTGGTCACGGACAAGGCCTTCGCGTACATTGGGCAATATGGGAAATCGA
TCAAAACTCTGTCTGTTGCCTTCTCTGGCAATACTGACATGTCACTCAGATATGTGTTTGAAGGATGCACTCGGTTGCAG
AAGCTTGAGGTCAGGGAATGTCCTTTTGGTGACGAGGGATTGCTCTCTGGTTTAAGCCACTTTTGGAATATGAGATTCTT
GTGGATGAGCTCTTGCAGAGTAACCATGACAGGCTGTAGATACGTAGCTCAGCAAATGCCAAATTTGGTGGCTGAAGTGA
TTAGTGGCCATTCTGGTAATGAAGATGTGACTGCCGATAATGTTGACCATCTGTATTTATATCGATCTCTTGCAGGACCA
AGGGACGACGCCCCTTCATTTGTCAAAATCTTG

Alignment

ORF - retro_oind_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.43 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLESVLEFLTAARDRNAASLVCRSWYRAEAQTRRELFIGNCYAVSPRRAVERFGGVRAVVLKGKPRFADF
          .LES.L.FLT.ARDRN.ASLVCR.WY.AEA.TR.ELFI.NCYAVSP.R..ERF.G.R...LKG.P.FAD.
Retrocopy LLESILQFLTTARDRNMASLVCRYWYHAEAETRQELFIRNCYAVSPNRVIERFRGLRSITLKGRPCFADS

Parental  SLVPYGWGAYVSPWVAALGPAYPLLERICLKRMTVSNDDLALIAKSFPLFKELSLVCCDGFSTLGLAAIA
          .LVP.GWG.Y.SPWVAALGPAYP.L..I.LKRMTVS..DL.LIA.SFP...ELSL..CD.FS..GLA.IA
Retrocopy TLVPKGWGGYASPWVAALGPAYPHLKCIFLKRMTVSDNDLRLIAQSFPQLRELSLMSCDKFSATGLAIIA

Parental  ERCRHLRVLDLIEDYIDEEEDELVDWISKFPESNTSLESLVFDCVSVPFNFEALEALVARSPAMRRLRMN
          E.CRHL.VLDLI.D......DE.VDWIS.FP...TSLESL.F.CV..P.NFE.LEALVARSP....L..N
Retrocopy EQCRHLHVLDLINDKVEDTVDEQVDWISMFPKPSTSLESLLFSCVDTPCNFESLEALVARSPGLCQLGVN

Parental  HHVTVEQLRRLMARAPQLTHLGTGAFRSEPG-PGGAL--SVTELATSFAASRSLICLSGFRDVNPEYLPA
          .HVTVEQL..LMA.AP.LTHLGTG.FRS..G.P.G....SV.ELAT.FAA.RSL..LSG..D.NP.YLPA
Retrocopy RHVTVEQLCCLMAIAPNLTHLGTGVFRSKTGYPAGEAPPSVSELATYFAACRSLHSLSGLQDANPDYLPA

Parental  IHPVCANLTSLNFSFANLTAEELTPIIRNCVRLRTFWVLDTVGDEGLRAVAETCSDLRELRVFPFDATED
          I.PVCANLTSLN.S.A.LT...L.PIIR.C..LRTF.V.D..GD.GL.A.AETC.DL..LRV........
Retrocopy IYPVCANLTSLNISSATLTGQQLAPIIRSCGNLRTFCVRDSIGDDGLSAIAETCLDLQDLRVYRLLRGSE

Parental  SEGSVSDVGLQAISEGCRKLESILYFCQRMTNAAVIAMSKNCSDLVTFRLCIMGRHRPDRITGEPMDDGF
          ...SVSDVGL..IS.GC.KL....Y.C..MTNAA...MS.NC..L..FRL.I.....PDRITGEPMD.GF
Retrocopy HHLSVSDVGLETISKGCQKLKTLTYYCGSMTNAAMVIMSSNCPNLEVFRLNILKTYLPDRITGEPMDEGF

Parental  GAIVMNCKKLTRLSVSGLLTDKAFAYIGKYGKLIKTLSVAFAGNSDMSLQSVFEGCTRLQKLEVRDSPFS
          GAIVMNCKKL.RLS.SGL.TDKAFAYIG.YGK.IKTLSVAF.GN.DMSL..VFEGCTRLQKLEVR..PF.
Retrocopy GAIVMNCKKLSRLSTSGLVTDKAFAYIGQYGKSIKTLSVAFSGNTDMSLRYVFEGCTRLQKLEVRECPFG

Parental  DKGLLSGLSYFYNMRFLWMNSCRLTMRGCRDVAQQMPDLVVEVMKDHLDDEG-EMETVDKLYLYRSLAGA
          D.GLLSGLS.F.NMRFLWM.SCR.TM.GCR.VAQQMP.LV.EV...H...E......VD.LYLYRSLAG.
Retrocopy DEGLLSGLSHFWNMRFLWMSSCRVTMTGCRYVAQQMPNLVAEVISGHSGNEDVTADNVDHLYLYRSLAGP

Parental  RNDAPSFVNIL
          R.DAPSFV.IL
Retrocopy RDDAPSFVKIL

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_74 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 sativa indica	BGIOSGA009088	1 retrocopy	retro_oind_74 ,