PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os04g01480.1
Common NameOsJ_13507, OSJNBa0094O15.14
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family C3H
Protein Properties Length: 851aa    MW: 92340.7 Da    PI: 4.9928
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g01480.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.41.1e-075283127
                      --S---SGGGGTS.....--TTTTT-SS-SSS CS
           zf-CCCH  1 yktelCrffartG.....tCkyGdrCkFaHgp 27
                      +kt+lC+ff+r        C++Gd+C++aH++
  LOC_Os04g01480.1 52 WKTSLCSFFRRRAassadGCSHGDSCRYAHSE 83
                      8**********88*****************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.106.5E-124889IPR000571Zinc finger, CCCH-type
SuperFamilySSF902298.63E-64988IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.3385184IPR000571Zinc finger, CCCH-type
PfamPF006421.7E-55283IPR000571Zinc finger, CCCH-type
CDDcd005901.91E-5127192No hitNo description
Gene3DG3DSA:3.30.70.3301.1E-6130201IPR012677Nucleotide-binding alpha-beta plait domain
SuperFamilySSF549283.29E-6130202IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS5168743.428245850IPR010280(Uracil-5)-methyltransferase family
SuperFamilySSF533352.72E-49247273IPR029063S-adenosyl-L-methionine-dependent methyltransferase
SuperFamilySSF533352.72E-49305408IPR029063S-adenosyl-L-methionine-dependent methyltransferase
SuperFamilySSF533352.72E-49467594IPR029063S-adenosyl-L-methionine-dependent methyltransferase
Gene3DG3DSA:3.40.50.1501.3E-62490594IPR029063S-adenosyl-L-methionine-dependent methyltransferase
PfamPF138472.0E-9534596IPR025714Methyltransferase domain
CDDcd024402.12E-7540594No hitNo description
Gene3DG3DSA:3.40.50.1501.3E-62733790IPR029063S-adenosyl-L-methionine-dependent methyltransferase
SuperFamilySSF533352.72E-49738850IPR029063S-adenosyl-L-methionine-dependent methyltransferase
PfamPF059581.0E-6743786IPR010280(Uracil-5)-methyltransferase family
PROSITE patternPS012300746778IPR030390RNA methyltransferase TrmA, active site
Gene3DG3DSA:3.40.50.1501.3E-62825850IPR029063S-adenosyl-L-methionine-dependent methyltransferase
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001510Biological ProcessRNA methylation
GO:0006396Biological ProcessRNA processing
GO:0000166Molecular Functionnucleotide binding
GO:0008173Molecular FunctionRNA methyltransferase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 851 aa     Download sequence    Send to blast
MEMEMEDNKA PSPPSPMESD VAGEKRKRED DASSSAVLAA ANNTGGAQHP MWKTSLCSFF  60
RRRAASSADG CSHGDSCRYA HSEEELRPRP DGTWDPTSDR AKKLRKVAAD EVEEEVVTID  120
DKALDKCLVG LPRGWANDRL KTFLQDKGIS YATAKKKKGM TVGFVTFENI EQLKNAIEVL  180
TENQSGGKEI KIADANRRSH QKLHTEKPVS DNGVTTENGT SVDVPPGETS APEAAISNKK  240
SVRDAVTPLA HMSYNDQLEH KKNSVAQILK RLTRNARKAC PTGIPLPDWV FKSKEIGGLP  300
CKLEGILESP VINGYRNKCE FSVGFSLEGK KTVGFMLGNF REGVTAVEEP VDCPNVSEIS  360
CKYALMFQDF LQSSSLPVWN RVDNCGFWRQ FTVREGRCQA QAVAQNAENQ ISEVMLIVQV  420
CSTGVDDAVM KDEFDKLTVA LQQGAATCSP PLPLTTIVVQ DHKGISNAAP ADCPLIPLLV  480
PKVDQSEGTV DKTRIHDHIG NLWFSISPTA FFQVNTLAAE RLYTLAGDWA NLNSGTLLFD  540
VCCGTGTIGL TLAHRVGMVV GIEMNESAVS DAERNALING VSNCRFVCGK AEDVMGSLLT  600
EYLGSPQQDI PVSEGAVSGT VKDEEVIDSS KNSGENLDSS MQKNDNGESQ QLGDAPADSS  660
SSAIDEIKGN SNDRVGNGLE GSHDEYNEVA GEDIHGEASL INESVDLKVS DCLEDRKTSD  720
DGSSISNNDV TAATACQFED IVAIVDPPRV GLHPTVIKAL RTHPRIRRLV YISCNPDSLV  780
ANAIELCTPS SEKQEKNKGN RGWRTMSSAG LARQRTKSMP NSEPFVPKRA MAVDLFPHTS  840
HCEMVMLFER *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5xj1_A4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5xj2_A4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5xj2_B4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5xj2_C4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5xj2_D4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5zq1_A4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5zq8_A4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
5zq8_B4e-16504601274371Uncharacterized RNA methyltransferase SP_1029
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.502170.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO379897790.0
Expression AtlasQ7XXI8-
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g01480.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g01480
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1201560.0AK120156.1 Oryza sativa Japonica Group cDNA clone:J013030B09, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636996.10.0zinc finger CCCH domain-containing protein 24 isoform X1
SwissprotQ8L7S30.0C3H24_ARATH; Zinc finger CCCH domain-containing protein 24
TrEMBLQ7XXI80.0Q7XXI8_ORYSJ; OSJNBa0094O15.14 protein
STRINGOGLUM04G00160.10.0(Oryza glumipatula)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP84933131
Representative plantOGRP60881112
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G28450.20.0C3H family protein
Publications ? help Back to Top
  1. Wang Y, et al.
    Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis.
    BMC Plant Biol., 2017. 17(1): p. 261
    [PMID:29268705]