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

Carubv10005558m

Common Name

CARUB_v10005558mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

MIKC_MADS

Protein Properties

Length: 255aa MW: 28929.5 Da PI: 9.8087

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10005558m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	99.8	1.1e-31	26	76	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyeys+ Carubv10005558m 26 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSN 76 79***********************************************95 PP
2	K-box	108.9	5.7e-36	93	190	3	100
K-box 3 kssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 +s++ s++e +a+++qqe+akL+++i ++q+++R+l+Ge ++s+s keL++Le +Le+s+++iRskKnell+++i+++qk+e +l+++n+ Lr+ Carubv10005558m 93 NSNTGSVAEINAQYYQQESAKLRQQIISIQNSNRQLMGETIGSMSPKELRNLEGRLERSITRIRSKKNELLFSEIDYMQKREVDLHNDNQILRA 186 45555699************************************************************************************** PP K-box 97 klee 100 k++e Carubv10005558m 187 KIAE 190 *986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.221	18	78	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.3E-40	18	77	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.58E-44	19	92	No hit	No description
SuperFamily	SSF55455	3.14E-33	19	91	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.9E-33	20	40	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	20	74	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	9.7E-27	27	74	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.9E-33	40	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.9E-33	55	76	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.7E-27	103	188	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.276	104	194	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0048366	Biological Process	leaf development
GO:0048440	Biological Process	carpel development
GO:0048443	Biological Process	stamen development
GO:0048497	Biological Process	maintenance of floral organ identity
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 255 aa Download sequence Send to blast
ITAYQAELGE DSSPLRKSGR GKIEIKRIEN TTNRQVTFCK RRNGLLKKAY ELSVLCDAEV 60 ALIVFSSRGR LYEYSNNSVK GTIERYKKAI SDNSNTGSVA EINAQYYQQE SAKLRQQIIS 120 IQNSNRQLMG ETIGSMSPKE LRNLEGRLER SITRIRSKKN ELLFSEIDYM QKREVDLHND 180 NQILRAKIAE NERNNPSISL MPGGSNYEQL MPPPQTQPQP FDSRNYFQVA ALQPNNHHYS 240 SAGGRQDQTA LQLV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1egw_A	5e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B	5e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C	5e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D	5e-20	19	86	1	68	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
3kov_A	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3kov_B	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3kov_I	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3kov_J	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_A	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_B	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_C	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_D	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_I	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
3p57_J	6e-20	19	86	1	68	Myocyte-specific enhancer factor 2A
6c9l_A	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_B	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_C	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_D	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_E	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
6c9l_F	6e-20	19	86	2	69	Myocyte-specific enhancer factor 2B
Search in ModeBase

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00609	ChIP-seq	Transfer from AT4G18960	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10005558m

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EU551772	0.0	EU551772.1 Capsella bursa-pastoris AGAMOUS-like protein (AGa) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_567569.3	0.0	K-box region and MADS-box transcription factor family protein, partial
Swissprot	P17839	0.0	AG_ARATH; Floral homeotic protein AGAMOUS
TrEMBL	R0F6V2	0.0	R0F6V2_9BRAS; Uncharacterized protein (Fragment)
STRING	XP_006284388.1	0.0	(Capsella rubella)

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-164	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Carubv10005558m
Entrez Gene	17878766

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]