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 Pta002089
Organism
Pinus taeda
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pinus; Pinus
Family C3H
Protein Properties Length: 361aa    MW: 40245.7 Da    PI: 8.2137
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
gnl|UG|Pta#S25798724PU_unrefUnigeneView CDS
PUT-157a-Pinus_taeda-1871PU_refplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH192.4e-06426326
               S---SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
               ++lC++f+  G C  G+ C F+H+
  Pta002089  4 RVLCKYFMH-GACLKGEACAFSHD 26
               79***8888.*************5 PP
2zf-CCCH28.82.1e-093454526
               --SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                C f++r G C+yG+rC++ H+
  Pta002089 34 VCTFYQR-GVCSYGSRCRYDHV 54
               6999999.*************7 PP
3zf-CCCH20.58.7e-07145165526
                --SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH   5 lCrffartGtCkyGdrCkFaHg 26 
                +C  fa+ G C++Gd+C+  Hg
  Pta002089 145 ICA-FAAAGKCPRGDTCPQLHG 165
                677.*****************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010314.258128IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-5227IPR000571Zinc finger, CCCH-type
SuperFamilySSF902299.16E-7426IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.108.7E-4629IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.0892956IPR000571Zinc finger, CCCH-type
SMARTSM003563.1E-43055IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.4E-53153IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.1E-43453IPR000571Zinc finger, CCCH-type
PfamPF006421.1E-63454IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.314140167IPR000571Zinc finger, CCCH-type
SMARTSM003560.0052141166IPR000571Zinc finger, CCCH-type
SuperFamilySSF578501.8E-10194273No hitNo description
Gene3DG3DSA:3.30.40.101.9E-9204274IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00243208268No hitNo description
PfamPF000971.7E-7209266IPR018957Zinc finger, C3HC4 RING-type
SMARTSM001841.0E-6209266IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.165209267IPR001841Zinc finger, RING-type
PROSITE patternPS005180233242IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010313.591296325IPR000571Zinc finger, CCCH-type
SMARTSM003560.069296324IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 361 aa     Download sequence    Send to blast
MSNRVLCKYF MHGACLKGEA CAFSHDWKDQ ENNVCTFYQR GVCSYGSRCR YDHVKVSHPE  60
STFSLSPISH LGSKVEPKSA SVHNGVTVGN DTSIAWHTGE LSGLSKPFFP PLGQAWTSGS  120
QDVSSTSRME LQTKSSIHDA ADLPICAFAA AGKCPRGDTC PQLHGDLCAT CGKHCLHPYR  180
PAEREEHIKQ CQHNQKRLEA LRNSQEIECS VCLDRVLSKP TAAERKFGLM SECDHPFCIS  240
CIRNWRGNNP VPGMDVNSVL RACPICRKLS HFVIPSVIWY SNQEEKQEII DNYKKKLSSI  300
DCKYFDFGKG TCPFGTSCFY KHAYNDGRRE EVKLRHLGAA DGSTVIAKNV RLSDFLGRLG  360
L
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pta.111930.0root| shoot| xylem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in dry seeds. Increased expression throughout imbibition and germination and when radicle and shoots are emerging. Up-regulated during cell differentiation. {ECO:0000269|PubMed:17870591}.
UniprotTISSUE SPECIFICITY: Expressed in primary roots and leaves. Detected in vascular bundle tissues. {ECO:0000269|PubMed:17870591}.
Functional Description ? help Back to Top
Source Description
UniProtE3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. {ECO:0000250}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011625473.11e-180E3 ubiquitin-protein ligase makorin
RefseqXP_011625474.11e-180E3 ubiquitin-protein ligase makorin
SwissprotQ5ZA071e-166C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A0D6R3J60.0A0A0D6R3J6_ARACU; Uncharacterized protein
STRINGERN117511e-177(Amborella trichopoda)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-124C3H 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. Sahi VP, et al.
    A molecular insight into Darwin's "plant brain hypothesis" through expression pattern study of the MKRN gene in plant embryo compared with mouse embryo.
    Plant Signal Behav, 2012. 7(3): p. 375-81
    [PMID:22499205]
  3. Wadekar HB,Sahi VP,Morita EH,Abe S
    MKRN expression pattern during embryonic and post-embryonic organogenesis in rice (Oryza sativa L. var. Nipponbare).
    Planta, 2013. 237(4): p. 1083-95
    [PMID:23262670]