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

Ciclev10030142m

Common Name

CICLE_v10030142mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

M-type_MADS

Protein Properties

Length: 225aa MW: 25119.9 Da PI: 9.7239

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10030142m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	69	4.3e-22	19	63	5	49
SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS SRF-TF 5 nksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49 n+sn qvtfskRr+g++KKA+EL++LC+a++a+i+fs+ k++ + Ciclev10030142m 19 NESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSF 63 89************************************9999887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	23.142	7	67	IPR002100	Transcription factor, MADS-box
SMART	SM00432	4.1E-31	7	66	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.57E-26	8	83	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.15E-34	8	77	No hit	No description
PRINTS	PR00404	4.5E-18	9	29	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.7E-24	18	63	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.5E-18	29	44	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.5E-18	44	65	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009960	Biological Process	endosperm development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 225 aa Download sequence Send to blast
MSSKKSKGRQ KVEMVKMPNE SNLQVTFSKR RTGLFKKASE LCTLCGADIA IIVFSPGKKV 60 FSFGHPCVET IVDRYLTRNP PQISGTMQLI EAHRNASVRE LNMQLTQVTV LNQLEIEKKR 120 GEELNQMRKA SQAQCWWEAP IEELNLPQLE QLKMSLEELK KNVGKQAEKM LIQSSNPPQF 180 FAGSSSNAGG MNLPFDPNNN ATVFNPNNMM PPPGYNPGFG HGFY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3kov_A	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3kov_B	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3kov_I	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3kov_J	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_A	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_B	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_C	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_D	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_I	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
3p57_J	2e-15	8	92	1	86	Myocyte-specific enhancer factor 2A
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during the syncytial endosperm development. {ECO:0000269\|PubMed:18334668}.
Uniprot	TISSUE SPECIFICITY: Expressed in the endosperm but not in the embryo. Detected in young siliques, roots, leaves, stems, young flowers and anthers. {ECO:0000269\|PubMed:18334668}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor. Required for suppression of cellularization and promotion of nuclear proliferation during early endosperm development. The FERTILIZATION-INDEPENDENT SEED (FIS) polycomb complex is required for suppression of ALG62 expression at the end of the syncytial phase of endosperm development. {ECO:0000269\|PubMed:18334668}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024034812.1	1e-163	agamous-like MADS-box protein AGL62
Swissprot	Q9FKK2	3e-71	AGL62_ARATH; Agamous-like MADS-box protein AGL62
TrEMBL	V4SG26	1e-165	V4SG26_9ROSI; Uncharacterized protein
STRING	XP_006422731.1	1e-166	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM86	28	390

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G60440.1	5e-73	AGAMOUS-like 62

Link Out ? help Back to Top
Phytozome	Ciclev10030142m
Entrez Gene	18033817

Publications ? help Back to Top
Xu W, et al. Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. Plant Cell, 2016. 28(6): p. 1343-60 [PMID:27233529] Figueiredo DD,Batista RA,Roszak PJ,Köhler C Auxin production couples endosperm development to fertilization. Nat Plants, 2015. 1: p. 15184 [PMID:27251719] Figueiredo DD,Batista RA,Roszak PJ,Hennig L,Köhler C Auxin production in the endosperm drives seed coat development in Arabidopsis. Elife, 2017. [PMID:27848912] Fiume E,Coen O,Xu W,Lepiniec L,Magnani E Growth of the Arabidopsis sub-epidermal integument cell layers might require an endosperm signal. Plant Signal Behav, 2017. 12(8): p. e1339000 [PMID:28613109] Zhang S, et al. FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development. Plant Physiol., 2018. 177(1): p. 285-299 [PMID:29523711]