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

Thecc1EG030175t1

Common Name

TCM_030175

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

HD-ZIP

Protein Properties

Length: 721aa MW: 78919.6 Da PI: 6.0831

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG030175t1	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	61.9	9.5e-20	57	112	1	56
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++ +++t+ q++e+e++F+++++p+ ++r+eL+++lgL+ qVk+WFqN+R+++k Thecc1EG030175t1 57 KKRYHRHTQLQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 112 688999***********************************************998 PP
2	START	223.9	5.1e-70	246	465	1	206
HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEE CS START 1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaet 81 ela +a++el+++a+++ep+Wv + +n+de+l++f+++ + ++ea+r+s+vv+m++++lve+l+d++ qW+ + +a+t Thecc1EG030175t1 246 ELAVAAMEELIRMAQSGEPLWVPGEkstDVLNEDEYLRTFPRGIGpkplgLRSEASRESAVVIMNHVNLVEILMDVN-QWSSAFCgivsRAMT 337 57899**************97777779*********999****************************.**99999 PP EEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEE CS START 82 levissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwv 167 lev+s+g galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+d+ ++ p + +++++pSg+li++++ng+skv+wv Thecc1EG030175t1 338 LEVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHTDGTWAVVDVSLDNLRPSP----MSKCRRRPSGCLIQELPNGYSKVIWV 426 *********************************************************99....788999**************** PP E-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 168 ehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206 ehv++++r +h+++r+lv+sgla+gak+wvatl+rqce+ Thecc1EG030175t1 427 EHVEVDDRAVHNIYRPLVNSGLAFGAKRWVATLDRQCER 465 ***********************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.0E-21	40	112	IPR009057	Homeodomain-like
SuperFamily	SSF46689	2.76E-19	42	114	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.633	54	114	IPR001356	Homeobox domain
SMART	SM00389	8.0E-19	55	118	IPR001356	Homeobox domain
CDD	cd00086	1.19E-18	57	115	No hit	No description
Pfam	PF00046	2.4E-17	57	112	IPR001356	Homeobox domain
PROSITE pattern	PS00027	0	89	112	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	45.211	237	468	IPR002913	START domain
SuperFamily	SSF55961	1.03E-36	237	467	No hit	No description
CDD	cd08875	9.60E-130	241	464	No hit	No description
SMART	SM00234	4.1E-71	246	465	IPR002913	START domain
Pfam	PF01852	5.0E-59	247	465	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	2.5E-6	318	465	IPR023393	START-like domain
SuperFamily	SSF55961	4.71E-27	485	716	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:0009845	Biological Process	seed germination
GO:0009913	Biological Process	epidermal cell differentiation
GO:0048497	Biological Process	maintenance of floral organ identity
GO:0048825	Biological Process	cotyledon development
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: 721 aa Download sequence Send to blast
MFSPNLFDSP HMFDMTHKTS EGELGKIRDD DYETKSGTET MDVPSGDEQD PNQRPKKKRY 60 HRHTQLQIQE MEAFFKECPH PDDKQRKELS RELGLEPLQV KFWFQNKRTQ MKAQHERHEN 120 AILKAENEKL RAENNRYKEA LSNATCPNCG GPAALGEMSF DEQHLRIENA RLREEIDRIS 180 GIAAKYVGKP LTSFPHISSH LHSRSLDPGA SNFGTQSGFV GEMYGGGDLL RSVSGPTEAD 240 KPMIVELAVA AMEELIRMAQ SGEPLWVPGE KSTDVLNEDE YLRTFPRGIG PKPLGLRSEA 300 SRESAVVIMN HVNLVEILMD VNQWSSAFCG IVSRAMTLEV LSTGVAGNYN GALQVMTAEF 360 QVPSPLVPTR ENYFVRYCKQ HTDGTWAVVD VSLDNLRPSP MSKCRRRPSG CLIQELPNGY 420 SKVIWVEHVE VDDRAVHNIY RPLVNSGLAF GAKRWVATLD RQCERLASSM ASNIPAGDLC 480 VITSPEGRKS MLKLAERMVT SFCTGVGAST AHAWTTLSAT GSDDVRVMTR KSMDDPGRPP 540 GIVLSAATSF WIPVPPKRVF DFLRDENSRS EWDILSNGGL VQEMAHIANG RDPGNCVSLL 600 RVNSANSSQS NMLILQESCS DATGSYVIYA PVDIVAMNVV LSGGDPDYVA LLPSGFAILP 660 DGPGLNGGGI LEIGSGGSLL TVAFQILVDS VPTAKLSLGS VATVNSLIKC TVERIKAAVA 720 *

Sequence ? help Back to Top

Protein Sequence Length: 721 aa Download sequence Send to blast

MFSPNLFDSP HMFDMTHKTS EGELGKIRDD DYETKSGTET MDVPSGDEQD PNQRPKKKRY  60
HRHTQLQIQE MEAFFKECPH PDDKQRKELS RELGLEPLQV KFWFQNKRTQ MKAQHERHEN  120
AILKAENEKL RAENNRYKEA LSNATCPNCG GPAALGEMSF DEQHLRIENA RLREEIDRIS  180
GIAAKYVGKP LTSFPHISSH LHSRSLDPGA SNFGTQSGFV GEMYGGGDLL RSVSGPTEAD  240
KPMIVELAVA AMEELIRMAQ SGEPLWVPGE KSTDVLNEDE YLRTFPRGIG PKPLGLRSEA  300
SRESAVVIMN HVNLVEILMD VNQWSSAFCG IVSRAMTLEV LSTGVAGNYN GALQVMTAEF  360
QVPSPLVPTR ENYFVRYCKQ HTDGTWAVVD VSLDNLRPSP MSKCRRRPSG CLIQELPNGY  420
SKVIWVEHVE VDDRAVHNIY RPLVNSGLAF GAKRWVATLD RQCERLASSM ASNIPAGDLC  480
VITSPEGRKS MLKLAERMVT SFCTGVGAST AHAWTTLSAT GSDDVRVMTR KSMDDPGRPP  540
GIVLSAATSF WIPVPPKRVF DFLRDENSRS EWDILSNGGL VQEMAHIANG RDPGNCVSLL  600
RVNSANSSQS NMLILQESCS DATGSYVIYA PVDIVAMNVV LSGGDPDYVA LLPSGFAILP  660
DGPGLNGGGI LEIGSGGSLL TVAFQILVDS VPTAKLSLGS VATVNSLIKC TVERIKAAVA  720
*

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1. {ECO:0000269\|PubMed:12505995}.

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	JN585951	1e-145	JN585951.1 Gossypium hirsutum HD-1A gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007026002.1	0.0	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_007026003.1	0.0	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_007026004.1	0.0	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Swissprot	Q93V99	0.0	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	A0A061GGE7	0.0	A0A061GGE7_THECC; Protodermal factor 2 isoform 1
STRING	EOY28624	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM491	28	149

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G04890.1	0.0	protodermal factor 2

Link Out ? help Back to Top
Phytozome	Thecc1EG030175t1
Entrez Gene	18597106

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] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444]