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

Carubv10008485m

Common Name

CARUB_v10008485mg

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

HD-ZIP

Protein Properties

Length: 687aa MW: 76373.7 Da PI: 6.4682

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10008485m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	60.2	3.2e-19	28	79	5	56
SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 5 ttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++t++q+++Le+ F+++++p++++r +L+++lgL rq+k+WFqNrR+++k Carubv10008485m 28 HRHTPHQIQRLESTFNECQHPDEKQRNQLSRELGLAPRQIKFWFQNRRTQKK 79 689**********************************************988 PP
2	START	151.2	8.7e-48	218	439	2	206
HHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS........SCEEEEEEEECCSCHHHHHHHHHCCCGG...CT-TT-SEEEEE CS START 2 laeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.......dsgealrasgvvdmvlallveellddke...qWdetlakaetl 82 +a +a++el+++ + +ep+W + e +n + + f++s + ++ea+r sgvv+ ++ +lv l+d+ + + + +a+ +tl Carubv10008485m 218 IAVTAMEELLRLLQTNEPLWITTEgcrEVLNLESYENLFPRSSSnggkkneLRMEASRSSGVVFTNALTLVDMLMDSVKsadFFPTIVAASKTL 311 6889********************8777777776777766668899**************************99988999999* PP EEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE- CS START 83 evissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwveh 169 +vissg al+lm elq+lsp+v+ R+f ++Ry++q + g+w+i+ vS + +q++++ R+ ++pSg+li+++sng+skvtwveh Carubv10008485m 312 AVISSGfrgnhgDALHLMIEELQVLSPMVAtREFCVLRYCQQIEHGTWAIANVSYEFPQFVSQ----SRSYRFPSGCLIQDMSNGYSKVTWVEH 401 *******9*********************************************95....56666****************** PP EE--SSXX.HHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 170 vdlkgrlp.hwllrslvksglaegaktwvatlqrqcek 206 v+ +++ p h++++ v++gla+ga +w +tlqr ce+ Carubv10008485m 402 VEFEEQEPiHEIFKDSVHKGLAFGAERWISTLQRMCER 439 **********************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	3.8E-19	11	81	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	7.2E-21	13	75	IPR009057	Homeodomain-like
PROSITE profile	PS50071	17.75	21	81	IPR001356	Homeobox domain
SMART	SM00389	4.1E-18	22	85	IPR001356	Homeobox domain
Pfam	PF00046	7.6E-17	28	79	IPR001356	Homeobox domain
CDD	cd00086	2.68E-18	28	82	No hit	No description
PROSITE pattern	PS00027	0	56	79	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	48.2	208	442	IPR002913	START domain
SuperFamily	SSF55961	4.12E-31	209	440	No hit	No description
CDD	cd08875	6.34E-104	212	438	No hit	No description
SMART	SM00234	4.0E-34	217	439	IPR002913	START domain
Pfam	PF01852	7.5E-40	218	439	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	1.7E-8	248	437	IPR023393	START-like domain
SuperFamily	SSF55961	6.04E-19	457	677	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010091	Biological Process	trichome branching
GO:0048497	Biological Process	maintenance of floral organ identity
GO:0005634	Cellular Component	nucleus
GO:0008289	Molecular Function	lipid binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 687 aa Download sequence Send to blast
MNMEFFGDSQ IHDGSETDKK NKKKKRFHRH TPHQIQRLES TFNECQHPDE KQRNQLSREL 60 GLAPRQIKFW FQNRRTQKKA QHERADNCAL KEENDKIRCE NIAIREAIKH AICPNCGDSP 120 VNEDSYFDEQ KLRIENAQLR DELERVSSIA AKFIGRPISH LPPLLNPMHV SPLELFHSGP 180 SLDFDLLPGS CSSMALPSLP SQPNLVLSEM DKSLMTNIAV TAMEELLRLL QTNEPLWITT 240 EGCREVLNLE SYENLFPRSS SNGGKKNELR MEASRSSGVV FTNALTLVDM LMDSVKSADF 300 FPTIVAASKT LAVISSGFRG NHGDALHLMI EELQVLSPMV ATREFCVLRY CQQIEHGTWA 360 IANVSYEFPQ FVSQSRSYRF PSGCLIQDMS NGYSKVTWVE HVEFEEQEPI HEIFKDSVHK 420 GLAFGAERWI STLQRMCERF TEPATSSLDL GGVIPSPEGK RSIMRLAHRM VSNFCLSVGT 480 SNNTRSTVVS GLDEFAIRVT SHKSLHEPNG MVLCAATSFW LPNSPQNVFN FLKDERTRPQ 540 WDVLSNGNPV QEVANIANGS NPGNCISVLR GFNVSSSQNN MLILQESCID SSSAALVIYT 600 PVDLPALNIA MSGQDTSCIP ILPSGFAISP DGSSKGGGSL ITVGFQIMVS GLQPAKLNME 660 SMETVNNLIN TTVHHIKTTL NCPSTA*

Sequence ? help Back to Top

Protein Sequence Length: 687 aa Download sequence Send to blast

MNMEFFGDSQ IHDGSETDKK NKKKKRFHRH TPHQIQRLES TFNECQHPDE KQRNQLSREL  60
GLAPRQIKFW FQNRRTQKKA QHERADNCAL KEENDKIRCE NIAIREAIKH AICPNCGDSP  120
VNEDSYFDEQ KLRIENAQLR DELERVSSIA AKFIGRPISH LPPLLNPMHV SPLELFHSGP  180
SLDFDLLPGS CSSMALPSLP SQPNLVLSEM DKSLMTNIAV TAMEELLRLL QTNEPLWITT  240
EGCREVLNLE SYENLFPRSS SNGGKKNELR MEASRSSGVV FTNALTLVDM LMDSVKSADF  300
FPTIVAASKT LAVISSGFRG NHGDALHLMI EELQVLSPMV ATREFCVLRY CQQIEHGTWA  360
IANVSYEFPQ FVSQSRSYRF PSGCLIQDMS NGYSKVTWVE HVEFEEQEPI HEIFKDSVHK  420
GLAFGAERWI STLQRMCERF TEPATSSLDL GGVIPSPEGK RSIMRLAHRM VSNFCLSVGT  480
SNNTRSTVVS GLDEFAIRVT SHKSLHEPNG MVLCAATSFW LPNSPQNVFN FLKDERTRPQ  540
WDVLSNGNPV QEVANIANGS NPGNCISVLR GFNVSSSQNN MLILQESCID SSSAALVIYT  600
PVDLPALNIA MSGQDTSCIP ILPSGFAISP DGSSKGGGSL ITVGFQIMVS GLQPAKLNME  660
SMETVNNLIN TTVHHIKTTL NCPSTA*

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that acts as negative regulator of trichome branching in association with HDG11 (PubMed:16778018). May regulate cell differentiation and proliferation during root and shoot meristem development (PubMed:25564655). Acts as positive regulator of SCL18/LAS expression (PubMed:25358340). {ECO:0000269\|PubMed:16778018, ECO:0000269\|PubMed:25358340, ECO:0000269\|PubMed:25564655}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10008485m

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	AB493465	0.0	AB493465.1 Arabidopsis thaliana At1g17920 mRNA for hypothetical protein, partial cds, clone: RAAt1g17920.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006306921.1	0.0	homeobox-leucine zipper protein HDG12
Swissprot	Q9LMT8	0.0	HDG12_ARATH; Homeobox-leucine zipper protein HDG12
TrEMBL	R0IBH0	0.0	R0IBH0_9BRAS; Uncharacterized protein
STRING	XP_006306921.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3004	26	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G17920.1	0.0	homeodomain GLABROUS 12

Link Out ? help Back to Top
Phytozome	Carubv10008485m
Entrez Gene	17897842

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Tian C, et al. An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation. Mol. Syst. Biol., 2014. 10: p. 755 [PMID:25358340] Horstman A, et al. AIL and HDG proteins act antagonistically to control cell proliferation. Development, 2015. 142(3): p. 454-64 [PMID:25564655]