PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

RrC4938_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

MIKC_MADS

Protein Properties

Length: 197aa MW: 22241.9 Da PI: 8.6217

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4938_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	100.4	6.9e-32	26	76	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyeys+ RrC4938_p2 26 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSN 76 79***********************************************95 PP
2	K-box	22.9	3.5e-09	104	136	68	100
K-box 68 kKnellleqieelqkkekelqeenkaLrkklee 100 +nell+++i+++qk+e +lq++n+ Lr+k++e RrC4938_p2 104 AQNELLFAEIDYMQKREADLQSDNQLLRAKIAE 136 589***************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.165	18	78	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.5E-41	18	77	IPR002100	Transcription factor, MADS-box
CDD	cd00265	4.59E-48	19	92	No hit	No description
SuperFamily	SSF55455	1.57E-33	19	93	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	20	74	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.9E-33	20	40	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	6.3E-27	27	74	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.9E-33	40	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.9E-33	55	76	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 197 aa Download sequence Send to blast
MAYQMELGGD SSPQRKSGGR GKIEIKRIEN TTNRQVTFCK RRNGLLKKAY ELSVLCDAEV 60 ALIVFSSRGR LYEYSNNSVK GTIERYKKAI SDNTNTGTVA EINAQNELLF AEIDYMQKRE 120 ADLQSDNQLL RAKIAENEGN NPSMNLMPGG YEQIMQPLQT QPQPFDSRNY FQVAALQPNN 180 HHYSSAGRQD QTALQLV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1egw_A	2e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B	2e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C	2e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D	2e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1tqe_P	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
1tqe_Q	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
1tqe_R	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
1tqe_S	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
3mu6_A	2e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3mu6_B	2e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3mu6_C	2e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3mu6_D	2e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
6c9l_A	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_B	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_C	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_D	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_E	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_F	2e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the control of organ identity during the early development of flowers. Is required for normal development of stamens and carpels in the wild-type flower. Plays a role in maintaining the determinacy of the floral meristem. Acts as C class cadastral protein by repressing the A class floral homeotic genes like APETALA1. Forms a heterodimer via the K-box domain with either SEPALATTA1/AGL2, SEPALATTA2/AGL4, SEPALLATA3/AGL9 or AGL6 that could be involved in genes regulation during floral meristem development. Controls AHL21/GIK, a multifunctional chromatin modifier in reproductive organ patterning and differentiation (PubMed:19956801). Induces microsporogenesis through the activation of SPL/NZZ (PubMed:15254538). {ECO:0000269\|PubMed:15254538, ECO:0000269\|PubMed:19956801}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by the A class floral homeotic protein APETALA2 and by other repressors like LEUNIG, SEUSS, SAP or CURLY LEAF. Positively regulated by both LEAFY and APETALA1. Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. Up-regulated by HUA2. {ECO:0000269\|PubMed:10198637, ECO:0000269\|PubMed:11058164, ECO:0000269\|PubMed:1675158, ECO:0000269\|PubMed:17794879, ECO:0000269\|PubMed:18281509, ECO:0000269\|PubMed:19783648, ECO:0000269\|PubMed:9783581}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KC984300	1e-127	KC984300.2 Brassica oleracea var. viridis AG mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018480894.1	1e-124	PREDICTED: floral homeotic protein AGAMOUS-like isoform X2
Refseq	XP_018480895.1	1e-124	PREDICTED: floral homeotic protein AGAMOUS-like isoform X3
Swissprot	P17839	1e-114	AG_ARATH; Floral homeotic protein AGAMOUS
TrEMBL	M4D7V4	1e-119	M4D7V4_BRARP; Uncharacterized protein
STRING	Bra012564.1-P	1e-120	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6181	22	37

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G18960.1	1e-116	MIKC_MADS family protein

Publications ? help Back to Top
Huang Z, et al. APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis thaliana. New Phytol., 2017. 215(3): p. 1197-1209 [PMID:27604611] Rong XF, et al. Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 756-764 [PMID:29186581] Uemura A, et al. Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis. Plant Reprod, 2018. 31(1): p. 89-105 [PMID:29218596]