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

Carubv10003004m

Common Name

CARUB_v10003004mg

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

SRS

Protein Properties

Length: 462aa MW: 48684.9 Da PI: 8.7745

Description

SRS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10003004m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF702	213	7e-66	251	414	2	154
DUF702 2 rsgtasCqdCGnqakkdCaheRCRtCCksrgfdCathvkstWvpaakrrerqqqlaaasskaaasa.aeaaskrkrelkskkqsalsstklssa 94 +sgta+CqdCGnqakk+C+++RCRtCCksrgfdC+thvkstWv+aa+rrerq + + a+ +a +s +++ +k++r s++q+a+s+t++s++ Carubv10003004m 251 ASGTATCQDCGNQAKKECKQRRCRTCCKSRGFDCSTHVKSTWVSAARRRERQVMPSGANPTAGSSLsTSSGTKKPRIVGSQQQQATSHTSTSNT 344 57999***********************************************9999998888877578889999999999999999998887 PP DUF702 95 eskkeletss...........lPeevsseavfrcvrvssvddgeeelaYqtavsigGhvfkGiLydqGlee 154 +++++etss +P +++++avf+cvrv++v++g++e+aYq++v+igGhvfkG+LydqGle Carubv10003004m 345 -PPQSFETSSsrqdgggsreaWPGQIRAAAVFKCVRVTAVEEGDDEYAYQAVVKIGGHVFKGFLYDQGLEP 414 .566788777799*******************************************************985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF05142	2.6E-58	254	413	IPR007818	Protein of unknown function DUF702
TIGRFAMs	TIGR01623	3.0E-26	256	298	IPR006510	Zinc finger, lateral root primordium type 1
TIGRFAMs	TIGR01624	1.5E-29	364	412	IPR006511	Lateral Root Primordium type 1, C-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009733	Biological Process	response to auxin
GO:0048364	Biological Process	root development
GO:0042803	Molecular Function	protein homodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 462 aa Download sequence Send to blast
MRMYRTMDLK RVKPMQPVLD GNKSRDRGAL KGKWSHAHER LCKREKSDQD PSEDLCNRCI 60 WVMYIGALCS VATTRRNNLP TSDSGAFTDW AAAATTTTTS SRATEDLSLG FNAGPAVVHG 120 GLGSASAAGV PSWPPGTSVR YGLPSSAAAT EMGMVGLRDV FLVAPAYHHH QNAGVLSGPE 180 AAAALGVGVV PLLTAGPPQQ NVEDTDINFL GNNRRWQNND NNHETQYLHF KSTNQTPVGT 240 SSNNSGSGSG ASGTATCQDC GNQAKKECKQ RRCRTCCKSR GFDCSTHVKS TWVSAARRRE 300 RQVMPSGANP TAGSSLSTSS GTKKPRIVGS QQQQATSHTS TSNTPPQSFE TSSSRQDGGG 360 SREAWPGQIR AAAVFKCVRV TAVEEGDDEY AYQAVVKIGG HVFKGFLYDQ GLEPKEGFPN 420 MSDLHLGGGA NNHNGVSASG PILDPPNVYG GGGGSGGGFY G*

Sequence ? help Back to Top

Protein Sequence Length: 462 aa Download sequence Send to blast

MRMYRTMDLK RVKPMQPVLD GNKSRDRGAL KGKWSHAHER LCKREKSDQD PSEDLCNRCI  60
WVMYIGALCS VATTRRNNLP TSDSGAFTDW AAAATTTTTS SRATEDLSLG FNAGPAVVHG  120
GLGSASAAGV PSWPPGTSVR YGLPSSAAAT EMGMVGLRDV FLVAPAYHHH QNAGVLSGPE  180
AAAALGVGVV PLLTAGPPQQ NVEDTDINFL GNNRRWQNND NNHETQYLHF KSTNQTPVGT  240
SSNNSGSGSG ASGTATCQDC GNQAKKECKQ RRCRTCCKSR GFDCSTHVKS TWVSAARRRE  300
RQVMPSGANP TAGSSLSTSS GTKKPRIVGS QQQQATSHTS TSNTPPQSFE TSSSRQDGGG  360
SREAWPGQIR AAAVFKCVRV TAVEEGDDEY AYQAVVKIGG HVFKGFLYDQ GLEPKEGFPN  420
MSDLHLGGGA NNHNGVSASG PILDPPNVYG GGGGSGGGFY G*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering. Synergistically with other SHI-related proteins, regulates gynoecium, stamen and leaf development in a dose-dependent manner, controlling apical-basal patterning. Promotes style and stigma formation, and influence vascular development during gynoecium development. May also have a role in the formation and/or maintenance of the shoot apical meristem (SAM). Modulates root growth. {ECO:0000269\|PubMed:16740146, ECO:0000269\|PubMed:18835563}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10003004m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expression repressed by LDL1 via histone H3 and H4 deacetylation. {ECO:0000269\|PubMed:18835563}.

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	BT020614	0.0	BT020614.1 Arabidopsis thaliana At5g12330 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023637004.1	0.0	protein LATERAL ROOT PRIMORDIUM 1
Swissprot	Q94CK9	1e-167	LRP1_ARATH; Protein LATERAL ROOT PRIMORDIUM 1
TrEMBL	R0HF13	0.0	R0HF13_9BRAS; Uncharacterized protein
STRING	XP_006289475.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5883	26	46

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G12330.4	0.0	Lateral root primordium (LRP) protein-related

Link Out ? help Back to Top
Phytozome	Carubv10003004m
Entrez Gene	17883640

Publications ? help Back to Top
Estornell LH,Landberg K,Cierlik I,Sundberg E SHI/STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis. Front Plant Sci, 2018. 9: p. 150 [PMID:29491878]