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 XP_009127893.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 397aa    MW: 45577.1 Da    PI: 8.0285
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009127893.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.10.000623557123
                    EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                    y C++Cg s s k++ ++Hi++H
  XP_009127893.1 35 YLCQYCGISRSKKYLITSHINSH 57
                    56********************6 PP
2zf-C2H220.21.6e-0682104123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C+ Cg  F+ + +Lk+H+++H
  XP_009127893.1  82 HTCQECGAEFKKPAHLKQHMQSH 104
                     79*******************99 PP
3zf-C2H2171.7e-05110134123
                     EEET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                     ++C   dC+ s++rk++L+rH+ tH
  XP_009127893.1 110 FECYvdDCTSSYRRKDHLNRHLLTH 134
                     789999*****************99 PP
4zf-C2H222.13.9e-07200223223
                     EET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                     +C+   Cgk F+ +s+L++H+ +H
  XP_009127893.1 200 VCKekGCGKAFKYPSQLQKHQDSH 223
                     79999****************998 PP
5zf-C2H218.55.6e-06290315123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                     +kC+   C+ +Fs  snL++H++  H
  XP_009127893.1 290 FKCEveGCSSTFSKASNLRKHLKAvH 315
                     89********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355253557IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-481101IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015714.00482109IPR007087Zinc finger, C2H2
SMARTSM003550.001582104IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SuperFamilySSF576671.31E-1094136No hitNo description
Gene3DG3DSA:3.30.160.607.1E-13102136IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.889110139IPR007087Zinc finger, C2H2
SMARTSM003550.2110134IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280112134IPR007087Zinc finger, C2H2
SuperFamilySSF576676.36E-5137165No hitNo description
PROSITE profilePS501579.743139169IPR007087Zinc finger, C2H2
SMARTSM003550.42139164IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280141164IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.8E-8188223IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.3E-6188224No hitNo description
PROSITE profilePS5015710.72199228IPR007087Zinc finger, C2H2
SMARTSM003550.0018199223IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280201223IPR007087Zinc finger, C2H2
SMARTSM003550.53231256IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.9E-4233254IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280233256IPR007087Zinc finger, C2H2
SMARTSM0035522259280IPR015880Zinc finger, C2H2-like
SuperFamilySSF576672.5E-9271328No hitNo description
PROSITE profilePS5015713.027290320IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.9E-8290315IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.2E-4290315IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280292315IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.1E-5316344IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.5321347IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280323347IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 397 aa     Download sequence    Send to blast
MQTNPDHRVE NQSEMAEEAA NVDAKPSKPK DIRHYLCQYC GISRSKKYLI TSHINSHHKM  60
EVEMERDEEA CEVDEEEVSG KHTCQECGAE FKKPAHLKQH MQSHSLERPF ECYVDDCTSS  120
YRRKDHLNRH LLTHKGKLFK CPVENCKSEF SVHGNISRHV KKFHSKDDGN KDDTGNSKKE  180
DTGNGDSHHS ESSTGQKKLV CKEKGCGKAF KYPSQLQKHQ DSHVKLDSIE AFCSEPGCMK  240
YFTNEECLKA HIRSYHQHIN CEICGSKHLK KNIKRHLRTH EEDSSSPGEF KCEVEGCSST  300
FSKASNLRKH LKAVHEDIRP FVCGFSGCAK RFAYKHVRNN HEKSGSHIYT CGDFVEADED  360
FTSRPRGGVK RKHVTAEMLI RKRVMPPQFD SQEHETC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5wjq_D2e-17353509284Zinc finger protein 568
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.92551e-158leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in 10-day-old seedlings (at protein level). In correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length isoform 1 protein TFIIIA with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts accumulate in various tissues of the reproductive phase, including flowers and siliques, but only isoform 2 is present in mature seeds. In flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at protein level). Very low amounts of TFIIIA are found in extracts from fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA protein progressively increases from fresh siliques to seeds concomitant with lower proportions of the shorter TFIIIA-C protein (at protein level) thus leading to 5S rRNA accumulation in the seed. {ECO:0000269|PubMed:22353599}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and seeds. {ECO:0000269|PubMed:22353599}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein (PubMed:22353599). Isoform 1 is a transcription activator the binds both 5S rDNA and 5S rRNA and stimulates the transcription of 5S rRNA gene (PubMed:12711688, PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development (PubMed:22353599). {ECO:0000269|PubMed:12711688, ECO:0000269|PubMed:22353599}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009127893.1
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_009127893.10.0PREDICTED: transcription factor IIIA
SwissprotQ84MZ40.0TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A398AH350.0A0A398AH35_BRACM; Uncharacterized protein
TrEMBLM4CUV90.0M4CUV9_BRARP; Uncharacterized protein
STRINGBra008004.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47142852
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.20.0transcription factor IIIA