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 Oropetium_20150105_03804A
Organism
Oropetium thomaeum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Cynodonteae; Tripogoninae; Oropetium
Family C3H
Protein Properties Length: 357aa    MW: 38907.5 Da    PI: 7.0859
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Oropetium_20150105_03804AgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH43.45.4e-14282307126
                                --S---SGGGGTS--TTTTT-SS-SS CS
                    zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                                +ktelC+ + +tG C+yGd C+FaHg
  Oropetium_20150105_03804A 282 FKTELCNKWEETGACQYGDHCQFAHG 307
                                79***********************8 PP
2zf-CCCH21.83.3e-07320345126
                                --S---SGGGGTS--TTTTT-SS-SS CS
                    zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                                ykte Cr  +++  C+yG rC+F H+
  Oropetium_20150105_03804A 320 YKTEVCRMVLAGILCPYGHRCHFRHS 345
                                9**********99**********997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.101.0E-17276314IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.14E-10278313IPR000571Zinc finger, CCCH-type
SMARTSM003562.4E-8281308IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.009281309IPR000571Zinc finger, CCCH-type
PfamPF006422.5E-11282307IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.2E-11315345IPR000571Zinc finger, CCCH-type
SuperFamilySSF902299.29E-8316346IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.169319347IPR000571Zinc finger, CCCH-type
SMARTSM003565.4E-5319346IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-4320345IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 357 aa     Download sequence    Send to blast
METLLPAAAQ LDGLHAAAFV PKPRVSSQPN LLANDGDLLC SGGGYSTHPL GREPERSASR  60
SPRARSSPHT GSVVDEEDDS PATAEHRARL ARSSPDTGSV VDEEDNSPAA AEHLARLALR  120
FQVEANRYQL CLSHLADTSD EAVALRREND QLRFDNGELV RRIATLGGQH SSAIALADEF  180
RRLTLAEEQA RAXXXXXXXX XXXXVMRPVP AAMPKSISVR STGYLKMNPS GKHRGPETNN  240
AGSQRVFVGL DGGGVKGQEK NGAEKEQGAG GVEFEVYNQG MFKTELCNKW EETGACQYGD  300
HCQFAHGIAE LRPVIRHPRY KTEVCRMVLA GILCPYGHRC HFRHSITPAD THLLHR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A4e-22282345467Butyrate response factor 2
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapOropetium_20150105_03804A
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0985712e-90AC098571.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1126_B10, complete sequence.
GenBankAC0988322e-90AC098832.3 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1268_B08, complete sequence.
GenBankAK1063542e-90AK106354.1 Oryza sativa Japonica Group cDNA clone:002-102-A03, full insert sequence.
GenBankAP0149612e-90AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
GenBankCP0126132e-90CP012613.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 5 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808834.11e-103zinc finger CCCH domain-containing protein 39-like
SwissprotQ6L5G11e-102C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLA0A2T7EA081e-102A0A2T7EA08_9POAL; Uncharacterized protein
TrEMBLA0A3L6R9Y51e-102A0A3L6R9Y5_PANMI; Zinc finger CCCH domain-containing protein 39-like
STRINGOPUNC05G24330.11e-101(Oryza punctata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP27753784
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G66810.11e-55C3H family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]