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

MDP0000233843

Common Name

LOC103448196, MADS16, MdJa1, MdJa2

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

M-type_MADS

Protein Properties

Length: 61aa MW: 6883.6 Da PI: 10.7083

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000233843	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	91.8	3.4e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+i n + rqvtfskRr g+lKKAeELSvLCda++a+iifsstgkl+ey+s MDP0000233843 9 KKIXNATARQVTFSKRRRGLLKKAEELSVLCDADIALIIFSSTGKLFEYAS 59 689**********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	30.137	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.3E-39	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	4.89E-34	2	60	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	3.4E-28	3	60	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	5.7E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	38	59	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: 61 aa Download sequence Send to blast
MAREKIQIKK IXNATARQVT FSKRRRGLLK KAEELSVLCD ADIALIIFSS TGKLFEYASS 60 X

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	2e-22	1	60	1	60	MEF2C
5f28_B	2e-22	1	60	1	60	MEF2C
5f28_C	2e-22	1	60	1	60	MEF2C
5f28_D	2e-22	1	60	1	60	MEF2C
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.13515	1e-90	bud

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During vegetative phase expressed in young leaves and apical meristem until early stage of bolting. Early in development of the inflorescence present in the coflorescence and flower primordia but not in the main apical meristem. Present throughout the floral meristem during early stages of flower development. Later disappears prior to emergence of sepal primordia. {ECO:0000269\|PubMed:19656343}.
Uniprot	TISSUE SPECIFICITY: Detected in roots and leaves. Expressed at very low levels in flowers and siliques. Present in floral meristems. {ECO:0000269\|PubMed:19656343}.
Uniprot	TISSUE SPECIFICITY: Widely expressed with highest levels in shoot tips and axillary buds. Also found in fully developed pedicels and flowers.

Functional Description ? help Back to Top
Source	Description
UniProt	Putative transcription factor that coordinates gene expression underlying the differentiation of the pedicel abscission zone. May also be involved in the maintenance of the inflorescence meristem state.
UniProt	Transcription repressor that inhibit floral transition in the autonomous flowering pathway, independent of photoperiod and temperature. Acts in a dosage-dependent manner. Together with AGL24 and AP1, controls the identity of the floral meristem and regulates expression of class B, C and E genes. Promotes EFM expression to suppress flowering (PubMed:25132385). {ECO:0000269\|PubMed:16679456, ECO:0000269\|PubMed:18694458, ECO:0000269\|PubMed:19656343, ECO:0000269\|PubMed:25132385}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the floral homeotic genes AP1 and SEP3 in emerging floral meristems. Up-regulated by HUA2. {ECO:0000269\|PubMed:15659097, ECO:0000269\|PubMed:17428825, ECO:0000269\|PubMed:18694458}.

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	LC004728	1e-87	LC004728.1 Malus domestica MdJa1 mRNA for JOINTLESS like protein MdJOINTLESSa, complete cds.
GenBank	LC004729	1e-87	LC004729.1 Malus domestica MdJa2 mRNA for JOINTLESS like protein MdJOINTLESSa, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024186163.1	8e-34	MADS-box protein SVP isoform X1
Refseq	XP_024186165.1	8e-34	MADS-box protein SVP isoform X1
Refseq	XP_024186166.1	7e-34	MADS-box protein SVP isoform X2
Refseq	XP_028954484.1	7e-34	MADS-box protein JOINTLESS isoform X2
Swissprot	Q9FUY6	1e-31	JOIN_SOLLC; MADS-box protein JOINTLESS
Swissprot	Q9FVC1	7e-32	SVP_ARATH; MADS-box protein SVP
TrEMBL	A0A2P6RPZ3	2e-32	A0A2P6RPZ3_ROSCH; Putative transcription factor MADS-MIKC family
STRING	XP_008385672.1	3e-33	(Malus domestica)
STRING	XP_004288518.1	4e-33	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF119	33	360

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G22540.1	3e-34	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	MDP0000233843
Entrez Gene	103448196

Publications ? help Back to Top
Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae). PLoS ONE, 2013. 8(6): p. e67243 [PMID:23840638] Jaudal M, et al. Overexpression of Medicago SVP genes causes floral defects and delayed flowering in Arabidopsis but only affects floral development in Medicago. J. Exp. Bot., 2014. 65(2): p. 429-42 [PMID:24249713] Müller-Xing R,Clarenz O,Pokorny L,Goodrich J,Schubert D Polycomb-Group Proteins and FLOWERING LOCUS T Maintain Commitment to Flowering in Arabidopsis thaliana. Plant Cell, 2014. 26(6): p. 2457-2471 [PMID:24920331] Nakano T,Kato H,Shima Y,Ito Y Apple SVP Family MADS-Box Proteins and the Tomato Pedicel Abscission Zone Regulator JOINTLESS have Similar Molecular Activities. Plant Cell Physiol., 2015. 56(6): p. 1097-106 [PMID:25746985] Hwan Lee J,Sook Chung K,Kim SK,Ahn JH Post-translational regulation of SHORT VEGETATIVE PHASE as a major mechanism for thermoregulation of flowering. Plant Signal Behav, 2014. 9(4): p. e28193 [PMID:25764420] Chen Z, et al. Overexpression of AtAP1M3 regulates flowering time and floral development in Arabidopsis and effects key flowering-related genes in poplar. Transgenic Res., 2015. 24(4): p. 705-15 [PMID:25820621] Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. BMC Plant Biol., 2015. 15: p. 41 [PMID:25848674] Müller-Xing R,Schubert D,Goodrich J Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(4): p. e1010868 [PMID:25924005] 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] Bechtold U, et al. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. Plant Cell, 2016. 28(2): p. 345-66 [PMID:26842464] Fernández V,Takahashi Y,Le Gourrierec J,Coupland G Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days. Plant J., 2016. 86(5): p. 426-40 [PMID:27117775] Wilson DC,Kempthorne CJ,Carella P,Liscombe DK,Cameron RK Age-Related Resistance in Arabidopsis thaliana Involves the MADS-Domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol. Plant Microbe Interact., 2017. 30(11): p. 919-929 [PMID:28812948] Zou YP, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol., 2017. 18(1): p. 239 [PMID:29284515] Richter R, et al. Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications. PLoS Genet., 2019. 15(4): p. e1008065 [PMID:30946745]