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 AT1G04990.1
Common NameF13M7.1
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C3H
Protein Properties Length: 404aa    MW: 44704.4 Da    PI: 8.1554
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G04990.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH33.76.1e-114873126
                 --S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH  1 yktelCrffartGtCkyGdrCkFaHg 26
                 ++++ C+f++rtG C yG++C+++H+
  AT1G04990.1 48 PGERDCQFYLRTGLCGYGSSCRYNHP 73
                 5789*********************9 PP
2zf-CCCH361.2e-1193117327
                  S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                  ++ C +f++tG CkyG++Ck++H++
  AT1G04990.1  93 QPDCEYFLKTGACKYGPTCKYHHPK 117
                  789********************96 PP
3zf-CCCH39.11.3e-12138162327
                  S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                  +++C++++rtGtC++G  CkF+H++
  AT1G04990.1 138 EKPCPYYLRTGTCRFGVACKFHHPQ 162
                  789********************97 PP
4zf-CCCH39.78.1e-13264287326
                  S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHg 26 
                  +++Crff+ tGtCkyGd Ck++H+
  AT1G04990.1 264 QPECRFFMNTGTCKYGDDCKYSHP 287
                  799********************8 PP
5zf-CCCH28.91.9e-09308334127
                  --S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                  ++++ C +f+ +G+Ck+G++CkF H++
  AT1G04990.1 308 PGQPACGNFRSYGFCKFGPNCKFDHPM 334
                  57899********************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003562.1E-54774IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.3524775IPR000571Zinc finger, CCCH-type
PfamPF006421.6E-84973IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.31E-55174IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.9E-45373IPR000571Zinc finger, CCCH-type
SMARTSM003561.7E-690117IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.90690118IPR000571Zinc finger, CCCH-type
PfamPF006422.3E-993117IPR000571Zinc finger, CCCH-type
SuperFamilySSF902296.02E-695118IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.1E-496116IPR000571Zinc finger, CCCH-type
SuperFamilySSF902297.33E-7134164IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.629135163IPR000571Zinc finger, CCCH-type
SMARTSM003567.4E-6135162IPR000571Zinc finger, CCCH-type
PfamPF006422.1E-10138162IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.109.2E-6139162IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010316.324261289IPR000571Zinc finger, CCCH-type
SMARTSM003561.7E-7262288IPR000571Zinc finger, CCCH-type
PfamPF006422.9E-10264287IPR000571Zinc finger, CCCH-type
SuperFamilySSF902292.35E-6266287IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.107.3E-6267286IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.96E-5303333IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.892307335IPR000571Zinc finger, CCCH-type
SMARTSM003563.1E-5307334IPR000571Zinc finger, CCCH-type
PfamPF006421.3E-7309334IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0090305Biological Processnucleic acid phosphodiester bond hydrolysis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003723Molecular FunctionRNA binding
GO:0004518Molecular Functionnuclease activity
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 404 aa     Download sequence    Send to blast
MRTPMSDTQH VQSSLVSIRS SDKIEDAFRK MKVNETGVEE LNPYPDRPGE RDCQFYLRTG  60
LCGYGSSCRY NHPTHLPQDV AYYKEELPER IGQPDCEYFL KTGACKYGPT CKYHHPKDRN  120
GAQPVMFNVI GLPMRLGEKP CPYYLRTGTC RFGVACKFHH PQPDNGHSTA YGMSSFPAAD  180
LRYASGLTMM STYGTLPRPQ VPQSYVPILV SPSQGFLPPQ GWAPYMAASN SMYNVKNQPY  240
YSGSSASMAM AVALNRGLSE SSDQPECRFF MNTGTCKYGD DCKYSHPGVR ISQPPPSLIN  300
PFVLPARPGQ PACGNFRSYG FCKFGPNCKF DHPMLPYPGL TMATSLPTPF ASPVTTHQRI  360
SPTPNRSDSK SLSNGKPDVK KESSETEKPD NGEVQDLSED ASSP
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.217430.0bud| flower| leaf| root
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453351130.0
Genevisible261125_at0.0
Expression AtlasAT1G04990-
AtGenExpressAT1G04990-
ATTED-IIAT1G04990-
Functional Description ? help Back to Top
Source Description
UniProtPossesses RNA-binding and ribonuclease activities in vitro. {ECO:0000269|PubMed:18582464}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G04990.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G04990
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4934340.0AB493434.1 Arabidopsis thaliana At1g04990 mRNA for hypothetical protein, partial cds, clone: RAAt1g04990.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001318923.10.0Zinc finger C-x8-C-x5-C-x3-H type family protein
RefseqNP_563725.10.0Zinc finger C-x8-C-x5-C-x3-H type family protein
RefseqNP_973759.10.0Zinc finger C-x8-C-x5-C-x3-H type family protein
SwissprotQ94AD90.0C3H3_ARATH; Zinc finger CCCH domain-containing protein 3
TrEMBLA0A384LLZ40.0A0A384LLZ4_ARATH; Uncharacterized protein
TrEMBLC0SUT10.0C0SUT1_ARATH; Uncharacterized protein At1g04990 (Fragment)
STRINGAT1G04990.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM23802675
Representative plantOGRP12471750
Publications ? help Back to Top
  1. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  2. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  3. Delaney KJ, et al.
    Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.
    Plant Physiol., 2006. 140(4): p. 1507-21
    [PMID:16500995]
  4. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]
  5. Addepalli B,Hunt AG
    Ribonuclease activity is a common property of Arabidopsis CCCH-containing zinc-finger proteins.
    FEBS Lett., 2008. 582(17): p. 2577-82
    [PMID:18582464]
  6. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  7. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]