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_013610995.1
Organism
Brassica oleracea
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 C3H
Protein Properties Length: 1885aa    MW: 205052 Da    PI: 4.3326
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013610995.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.61.7e-0618611884225
                      -S---SGGGGTS--TTTTT-SS-S CS
         zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                      +++ C+f++++G C+ G+ C++ H
  XP_013610995.1 1861 GQRVCKFHRENGNCRKGAACTYLH 1884
                      6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.40.102.2E-10716776IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF579031.55E-7717772IPR011011Zinc finger, FYVE/PHD-type
PROSITE profilePS500168.689720786IPR019787Zinc finger, PHD-finger
SMARTSM002491.8E-8722768IPR001965Zinc finger, PHD-type
CDDcd155681.16E-21722767No hitNo description
PROSITE patternPS013590723783IPR019786Zinc finger, PHD-type, conserved site
Gene3DG3DSA:1.10.245.103.2E-249171010IPR003121SWIB/MDM2 domain
SuperFamilySSF475923.92E-209261007IPR003121SWIB/MDM2 domain
SMARTSM001510.00499421007IPR019835SWIB domain
PfamPF022011.0E-129441002IPR003121SWIB/MDM2 domain
SMARTSM007192.2E-5310631172IPR004343Plus-3 domain
PROSITE profilePS5136030.44110631195IPR004343Plus-3 domain
SuperFamilySSF1590428.89E-3510641192IPR004343Plus-3 domain
PfamPF031265.7E-2410681170IPR004343Plus-3 domain
SuperFamilySSF552776.54E-1913991466IPR003169GYF domain
CDDcd000721.56E-1914131470No hitNo description
PROSITE profilePS5082916.8114131467IPR003169GYF domain
SMARTSM004441.8E-2314141469IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.7E-1714141467IPR003169GYF domain
PfamPF022133.1E-1414151456IPR003169GYF domain
PROSITE profilePS5010313.13118591885IPR000571Zinc finger, CCCH-type
PfamPF006422.0E-418611884IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010964Biological Processregulation of chromatin silencing by small RNA
GO:0032776Biological ProcessDNA methylation on cytosine
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
GO:0042393Molecular Functionhistone binding
Sequence ? help Back to Top
Protein Sequence    Length: 1885 aa     Download sequence    Send to blast
MDSDSAKASV ESMRDDPECI RVSNDPNLTG PCGESSAAAE EGGGCDGATG AKGIDAVDTA  60
AAVLNPVAEM SGVVDAVSAD LSPAAAEGGG GGGEEDAGFV AQECGSLDLV GGSAAVEVVP  120
PVVGEGGEED RAAKQSDSAA NLLGLGSEKV SISGEEPPSF DLPASEVNGD DSLREGSQEV  180
VCGGMADEKS SQAIESKLGQ DTESEKEKVD VMEEDTAAQA ASLEDIVSVD IDIPDVKDVA  240
SVAGFTEISS QDKGLGDSVP LERGPLKELQ IGEEARDLTD EDAKEDMDVT GGAMGNQLLK  300
TTEEEEKPEL EIKTKPQDVA DEGSEKNENR VGESSVDKET VIDDVKEDFE KDPEAGKSVG  360
MHVPESAEEV ETYVKYGDGI EEEGEGMAGV GEAELTVDLE ETQKLSEELA KVDETKIAEA  420
SEETGTVIRH EDEEKMDDMT DMAEDVKIHG DSSIADIEGG REDLEEMGVT EALEETVTDK  480
VEGAKIDEVS EETETRIEDE DQEKDDDMAD VKTHGDSLVA DIEEGKEIQE EMGLAEMTET  540
QEETVEGKAV RTKVAEASEE TETRSVDVDQ EKDENMMDVK TLGDSSVADT EEEKKRQEEM  600
GMAEMTETQE ESVEGKVDGT KASEMSEETE ARTEDEDEDE EKDENMTDAE THVDSSLADI  660
EEGKESQEEI EMTELTATQD ESVTAETGDE DAEDVEEENK GVGGKRKRVR NTKTGKKKEE  720
DVCFICFDGG DLVLCDRRGC PKAYHPSCVN QDEDFFRSKG KWNCGWHQCS KCEKTATYLC  780
YTCVFSLCKG CAKDAVFFCI RGNKGLCETC METIKLIERE EQEKKEPAQL DFDDKTSWES  840
LFKDYWIDLK TQLSISPEEL DQAKSPQKGN KSHAGKQGTA REVDYVTDEG SDSDSSPKKK  900
KTRSRSKSGS AEKNQSPANK SSSGETWASK ELLDVVAHMR RGDKSFLPST EVHALLLDYI  960
KKYNLRDPRR KSQVVCDSRL KNLFGKSHVG HFEMLNILDT HFLDKEQQQA DNIQGSIVDT  1020
DPDYVDLDEN VDHPVKSGKD KKRKTRKKGA RKGRQSNLDD FAAVDMHNIN LIYLRRSLVE  1080
DLLEDSTAFE EKVASAFVRL RISGNQKQDL YRLVQVVGTG KAPEPYKVGK KTTDYVLEIL  1140
NLDKTEVISI DIISNQDFTE DECNRLRQSI KCGLINRLTV GDIQEKAIAL QEVRVKNLLD  1200
AEILRFSHLR DRASDMGHRK ELRECVEKVQ LLKSPEERQR RLEEIPEIHA DPKMDPDYES  1260
EDEDEKEEKE KEKSLRRRSS SFNRRGRDPI SPRKGGFSSN ESWTGTSSYS STSAIRELSR  1320
SYSGRGSNGR GDYLGSSDDK VSDSLWNSGR EREKDMQHYL GSEKPRTVSL PEPPPRSSRA  1380
VAPPELSPRI APVISTPPPP VVPQPTPKSN ESEKMWHYKD PSGKVQGPFS MAQLRKWNNT  1440
GYFPAKLEIW KANESSLDSV LLTDALAGLF QKQGQSVDNS YPKAYSGQSS QSEPNIGSSA  1500
RTAPSVLDVP KNSQDTWSSG GSLPSPTPTQ MTTPTAKRRN FESRWSPTKP SAQSAVQSMS  1560
FPSAQSVPSQ ASRTDIPVVV NSAGALQPGT HPIPTPDRAN VSVNHYGSSA PLPSPTPVGG  1620
MQSWGNMQTD KFDSHGRGRG DAPFSSQNTS ASYGTTTPSA LTSQSQPGFP ASDPWRAPVP  1680
SQSNTQAQAP AWGMNNSQNS GQPQAPTNQN SSWGQATVVN PNMGWAGPPQ AGMSVNWAAS  1740
SVPPTGQGMP NPGWGGTAQV QQPQAYSANS GWGVTGQAQS QAQVQAPGSS TSPGWMQTGQ  1800
GMQSGNSNQN WGTQNQSAMQ SGGSGGNQTG YWGNQQNQNG DSGYGWNRQS SGSGGHNNFK  1860
GQRVCKFHRE NGNCRKGAAC TYLHN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A3e-19710796488Histone-lysine N-methyltransferase NSD3
4gnd_C3e-19710796488Histone-lysine N-methyltransferase NSD3
4gne_A3e-19710796488Histone-lysine N-methyltransferase NSD3
4gnf_A3e-19710796488Histone-lysine N-methyltransferase NSD3
4gng_A3e-19710796488Histone-lysine N-methyltransferase NSD3
4gng_D3e-19710796488Histone-lysine N-methyltransferase NSD3
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, mostly in the vasculature and shoot apices of young seedlings. {ECO:0000269|PubMed:22940247}.
Functional Description ? help Back to Top
Source Description
UniProtPlays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences. Involved in a chromatin-based RNA silencing pathway that encompasses both post-transcriptional gene silencing (PTGS) (e.g. RDR1, RDR6 and AGO2) and transcriptional gene silencing (TGS) (e.g. siRNA-dependent DNA methylation and histone H3) components. Mediates siRNA accumulation at specific chromatin loci. Binds H3K4me0 through its PHD to enforce low levels of H3K4 methylation and gene silencing at a subset of genomic loci. {ECO:0000269|PubMed:22940247}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013610995.1
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_013610995.10.0PREDICTED: zinc finger CCCH domain-containing protein 19
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLA0A0D3E3130.0A0A0D3E313_BRAOL; Uncharacterized protein
STRINGBo9g024110.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM54221620
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G16485.10.0nucleic acid binding;zinc ion binding;DNA binding