PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID HL.SW.v1.0.G015598.1
Organism
Humulus lupulus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Cannabaceae; Humulus
Family C3H
Protein Properties Length: 80aa    MW: 9083.34 Da    PI: 8.0762
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
HL.SW.v1.0.G015598.1genomeHOPBASEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH31.82.5e-101437225
                          -S---SGGGGTS--TTTTT-SS-S CS
               zf-CCCH  2 ktelCrffartGtCkyGdrCkFaH 25
                          ++++C+f+++ G C++GdrC++ H
  HL.SW.v1.0.G015598.1 14 DRVNCPFYFKIGACRHGDRCSRLH 37
                          689********************* PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.1121240IPR000571Zinc finger, CCCH-type
SMARTSM003560.00651339IPR000571Zinc finger, CCCH-type
PfamPF006425.3E-81437IPR000571Zinc finger, CCCH-type
SuperFamilySSF902297.06E-51641IPR000571Zinc finger, CCCH-type
PRINTSPR018486.4E-211837IPR009145U2 auxiliary factor small subunit
PRINTSPR018486.4E-213757IPR009145U2 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:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 80 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHTKP SISPTLLLSN MYQRPDMLTT  60
PGVDTQGQSL DPRKIQDNFE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A6e-24180174Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010096852.13e-52splicing factor U2af small subunit B
RefseqXP_010113116.18e-55splicing factor U2af small subunit B
SwissprotQ9S7096e-47U2AFA_ARATH; Splicing factor U2af small subunit A
TrEMBLA0A2P5C4W41e-51A0A2P5C4W4_PARAD; U2 auxiliary factor small subunit
TrEMBLW9SF682e-53W9SF68_9ROSA; Splicing factor U2af small subunit A
STRINGXP_010096852.11e-51(Morus notabilis)
STRINGXP_010113116.13e-54(Morus notabilis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF2540922
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.13e-33C3H family protein
Publications ? help Back to Top
  1. Day IS, et al.
    Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing.
    Plant J., 2012. 71(6): p. 936-47
    [PMID:22563826]
  2. Kim DW,Jeon SJ,Hwang SM,Hong JC,Bahk JD
    The C3H-type zinc finger protein GDS1/C3H42 is a nuclear-speckle-localized protein that is essential for normal growth and development in Arabidopsis.
    Plant Sci., 2016. 250: p. 141-153
    [PMID:27457991]
  3. Park HY, et al.
    The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms.
    Plant Cell Rep., 2017. 36(7): p. 1113-1123
    [PMID:28432478]