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 Sobic.004G178300.1.p
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family C3H
Protein Properties Length: 749aa    MW: 85335.2 Da    PI: 8.6831
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.004G178300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.91.5e-07230249625
                           -SGGGGTS--TTTTT-SS-S CS
               zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                           C+f+++tG C++G rC++ H
  Sobic.004G178300.1.p 230 CPFHLKTGACRFGVRCSRVH 249
                           ******************99 PP
2zf-CCCH24.26e-08359386126
                           --S---SGGGGTS..--TTTTT-SS-SS CS
               zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                           +k ++C +++r+   tC++G  C+F+H+
  Sobic.004G178300.1.p 359 WKAAICGDYMRSRykTCSHGVACNFIHC 386
                           7889***********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010311.807224252IPR000571Zinc finger, CCCH-type
SMARTSM003562225251IPR000571Zinc finger, CCCH-type
PfamPF006421.9E-5229249IPR000571Zinc finger, CCCH-type
PRINTSPR018489.0E-38230249IPR009145U2 auxiliary factor small subunit
PRINTSPR018489.0E-38249269IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010210.138256356IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3306.6E-25256354IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125406.74E-50257354No hitNo description
SMARTSM003612.8E-7271352IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018489.0E-38285300IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549282.31E-17287355IPR012677Nucleotide-binding alpha-beta plait domain
PfamPF000761.8E-4293349IPR000504RNA recognition motif domain
PRINTSPR018489.0E-38313335IPR009145U2 auxiliary factor small subunit
PRINTSPR018489.0E-38340364IPR009145U2 auxiliary factor small subunit
SMARTSM003560.044358387IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010310.662358388IPR000571Zinc finger, CCCH-type
PfamPF006421.3E-5359386IPR000571Zinc finger, CCCH-type
PRINTSPR018489.0E-38378390IPR009145U2 auxiliary factor small subunit
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000398Biological ProcessmRNA splicing, via spliceosome
GO:0089701Cellular ComponentU2AF
GO:0000166Molecular Functionnucleotide binding
GO:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 749 aa     Download sequence    Send to blast
MSSAVTAGGG AAAADGAPEA AATALTRREK RRERKKERRR RARREAAARA RAAAEAEAPA  60
ATDPEEERRL LEIQEAEAAA ESERARLAFE DAERRWLEAA AARAAEKAAA AAAEEEARAA  120
EASARKEPKD DQGNQSEEDS EWEYVEDGPA EIIWKGNEII VKKKKVKVPK GSKEKLPVQE  180
EDRPTSNPLP PQSVAFAAQR REPSLSAQEV LDKVAQETPN FGTEQDKAHC PFHLKTGACR  240
FGVRCSRVHF YPDKSSTLLM KNMYNGPGLA LDQDEGLEFT DEEIEQSYEE FYEDVHTEFL  300
KFGELVNFKV CRNGCFHLRG NVYVHYKSLD SALLAYSSMN GRYFAGKQIT CEFVAVTRWK  360
AAICGDYMRS RYKTCSHGVA CNFIHCFRNP GGDYEWADWD NPPPRYWIRK MTALFGPSVD  420
TMYEKESDTP NFKSSEGSDR KKLKISSNRY VSRGSRDEDV HTRHSQDYSH SKQEHSSHSM  480
NYEYKRHRRD SSSVDKHRRR DVEDTNGRQF STMENDSESH RHKHEERHRS DHGNGEKKDD  540
KTRPRKHCSD RRGSLEPGYS DWPSDFTDTD IRKGSSGEKS TSRYEYDDAK RSRRGSSEYY  600
NLERHHSTAQ KPTGKEHNTK RRSRRDIEDY YHDEKDGGRG KSRKHDRWVA TNSDVDSDVD  660
RYQSSSCKGT RSGRKEDAHP DSEAWHQRSS RSTKDDRRRK RHSGTEEGTS ESSSGDLSSD  720
SGSRRSRSSE NFSAHRSKRK RSVGKKSS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-322213859167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
13038RRERKKERR
23744RRRRARRE
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.004G178300.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJF6811440.0JF681144.1 Zea mays RGH3 splicing factor mRNA, complete cds.
GenBankJN7914190.0JN791419.1 Zea mays rough endosperm 3 alpha isoform (Rgh3) mRNA, complete cds, alternatively spliced.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002453991.20.0zinc finger CCCH domain-containing protein 16 isoform X2
SwissprotQ6YVX90.0C3H16_ORYSJ; Zinc finger CCCH domain-containing protein 16
TrEMBLA0A1Z5RNF90.0A0A1Z5RNF9_SORBI; Uncharacterized protein
STRINGSb04g022810.10.0(Sorghum bicolor)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.13e-11C3H 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]