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 Thecc1EG019508t1
Common NameTCM_019508
Organism
Theobroma cacao
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family RAV
Protein Properties Length: 317aa    MW: 36131.8 Da    PI: 9.788
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG019508t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP2476.3e-153583155
               AP2  1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55
                      s++kGV   + +grW A+I++      ++r++lg+f  +eeAaka++ a+++++g
  Thecc1EG019508t1 35 SKFKGVVSQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAAKAYDIAALRFRG 83
                      79****8888.8*********3.....5*************************98 PP
2B385.25.6e-27166254185
                       EEEE-..-HHHHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                       f+kv tpsdv+k++r+v+pk++a+++    +g+  +++ l +ed  g++W+++++y+k+s++yvltk W +Fvk+++Lk+gD v F ++
  Thecc1EG019508t1 166 FEKVATPSDVGKLNRIVIPKQHADKYfplqSGIVSKGVLLNFEDNMGQVWRFRYCYWKSSQSYVLTKDWTRFVKEKKLKAGDAVSFWRS 254
                       89****************************5566799*************************************************854 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541712.75E-173593IPR016177DNA-binding domain
CDDcd000189.54E-263593No hitNo description
PfamPF008473.6E-93583IPR001471AP2/ERF domain
SMARTSM003801.0E-263697IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.106.7E-213691IPR001471AP2/ERF domain
PROSITE profilePS5103219.8753691IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.6E-35162268IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.19E-27164260IPR015300DNA-binding pseudobarrel domain
CDDcd100174.26E-24165263No hitNo description
SMARTSM010196.5E-20166268IPR003340B3 DNA binding domain
PfamPF023621.3E-24166253IPR003340B3 DNA binding domain
PROSITE profilePS5086311.984166269IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 317 aa     Download sequence    Send to blast
MATYSSFPAR KFPENSCQSS ERSIEAAGPQ KQPSSKFKGV VSQPNGRWGA QIYEKHQRVW  60
LGTFNEEEEA AKAYDIAALR FRGQNAFTNF KPSIHTTDED DFEQFFLVSH SKEEIVDMIR  120
KHTYTNELEH SKYNYACHDT RKGIKGNGFS SLPGFDPFEG AREYLFEKVA TPSDVGKLNR  180
IVIPKQHADK YFPLQSGIVS KGVLLNFEDN MGQVWRFRYC YWKSSQSYVL TKDWTRFVKE  240
KKLKAGDAVS FWRSVGPNTK LFIGHKAGNV SNLEELPNRV VPRENSGVIR LFGVNILETN  300
MAVVSRKSKT KEKSLE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A5e-4616327411123DNA-binding protein RAV1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2. {ECO:0000269|PubMed:18718758}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing a peak at dawn. {ECO:0000269|PubMed:18718758}.
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_007033326.20.0PREDICTED: AP2/ERF and B3 domain-containing transcription factor RAV1
SwissprotQ9C6M51e-101RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A061EIM10.0A0A061EIM1_THECC; AP2 domain class transcription factor, putative
STRINGEOY042520.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM84827121
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G25560.11e-103RAV family protein
Publications ? help Back to Top
  1. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Choi D, et al.
    iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis.
    Mol Plant, 2014. 7(5): p. 792-813
    [PMID:24380880]
  4. Sgamma T,Jackson A,Muleo R,Thomas B,Massiah A
    TEMPRANILLO is a regulator of juvenility in plants.
    Sci Rep, 2014. 4: p. 3704
    [PMID:24424565]
  5. Matías-Hernández L,Aguilar-Jaramillo AE,Marín-González E,Suárez-López P,Pelaz S
    RAV genes: regulation of floral induction and beyond.
    Ann. Bot., 2014. 114(7): p. 1459-70
    [PMID:24812253]
  6. Marín-González E, et al.
    SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures.
    Plant Physiol., 2015. 169(2): p. 1214-24
    [PMID:26243615]
  7. Matías-Hernández L, et al.
    TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation.
    Plant Physiol., 2016. 170(3): p. 1624-39
    [PMID:26802039]