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

Csa13g052770.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina

Family

HD-ZIP

Protein Properties

Length: 746aa MW: 81582.1 Da PI: 5.7423

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa13g052770.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	61.2	1.6e-19	63	118	1	56
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l+L+ qVk+WFqN+R+++k Csa13g052770.1 63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLNLEPLQVKFWFQNKRTQMK 118 688999***********************************************998 PP
2	START	220.8	4.5e-69	253	473	1	206
HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEE CS START 1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetle 83 ela +a++elv++a+a +p+Wv+ e++n++e+ ++f+++ + ++ea+r+s+vv+m++ +lve+l+d++ qW+ + +a tle Csa13g052770.1 253 ELAVAAMEELVRMAQAVDPLWVSTDssmEILNEEEYFRTFPRGIGpkplgLRSEASRESAVVIMNHINLVEILMDVN-QWSCVFSgivsRALTLE 346 57899***************988899**********999****************************.************* PP EECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE CS START 84 vissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvd 171 v+s+g galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds ++ + ++ R +++pSg+li++++ng+skvtw+eh++ Csa13g052770.1 347 VLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPST---PILRTRRRPSGCLIQELPNGYSKVTWIEHME 438 ******************************************************976...7************************** PP --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206 +++r++h+++r+lv+sgla+gak+wvatl+rqce+ Csa13g052770.1 439 VDDRSVHNMYRPLVHSGLAFGAKRWVATLERQCER 473 *******************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.2E-23	44	118	IPR009057	Homeodomain-like
SuperFamily	SSF46689	8.36E-19	51	120	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.957	60	120	IPR001356	Homeobox domain
SMART	SM00389	1.0E-17	61	124	IPR001356	Homeobox domain
Pfam	PF00046	3.7E-17	63	118	IPR001356	Homeobox domain
CDD	cd00086	3.60E-18	63	121	No hit	No description
PROSITE pattern	PS00027	0	95	118	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	45.162	244	476	IPR002913	START domain
SuperFamily	SSF55961	1.21E-35	246	475	No hit	No description
CDD	cd08875	6.58E-126	248	472	No hit	No description
SMART	SM00234	7.0E-77	253	473	IPR002913	START domain
Pfam	PF01852	1.8E-58	254	473	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	1.1E-7	350	473	IPR023393	START-like domain
SuperFamily	SSF55961	5.31E-26	492	731	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: 746 aa Download sequence Send to blast
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG AEVTTENPSG EELQDPNQRP 60 NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN LEPLQVKFWF QNKRTQMKAQ 120 SERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE 180 EIDRISAIAA KYVGKPLGSS FAPLAIHAPS RSLDLEVGNF GNQTGFGGEM YGTGDILRSV 240 SIPSDTDKPI IVELAVAAME ELVRMAQAVD PLWVSTDSSM EILNEEEYFR TFPRGIGPKP 300 LGLRSEASRE SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL 360 QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPSTPIL RTRRRPSGCL 420 IQELPNGYSK VTWIEHMEVD DRSVHNMYRP LVHSGLAFGA KRWVATLERQ CERLASSMAS 480 NIPGDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM 540 DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP 600 GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG GDPDYVALLP 660 SGFAILPDGS VGGGDGNHQE VVSSTSFGSC GGSLLTVAFQ ILVDSVPTAK LSLGSVATVN 720 SLIKCTVERI KAAVACDNGG AGGGA*

Sequence ? help Back to Top

Protein Sequence Length: 746 aa Download sequence Send to blast

MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG AEVTTENPSG EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN LEPLQVKFWF QNKRTQMKAQ  120
SERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPLGSS FAPLAIHAPS RSLDLEVGNF GNQTGFGGEM YGTGDILRSV  240
SIPSDTDKPI IVELAVAAME ELVRMAQAVD PLWVSTDSSM EILNEEEYFR TFPRGIGPKP  300
LGLRSEASRE SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL  360
QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPSTPIL RTRRRPSGCL  420
IQELPNGYSK VTWIEHMEVD DRSVHNMYRP LVHSGLAFGA KRWVATLERQ CERLASSMAS  480
NIPGDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM  540
DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP  600
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG GDPDYVALLP  660
SGFAILPDGS VGGGDGNHQE VVSSTSFGSC GGSLLTVAFQ ILVDSVPTAK LSLGSVATVN  720
SLIKCTVERI KAAVACDNGG AGGGA*

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa13g052770.1

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	AF424560	0.0	AF424560.1 Arabidopsis thaliana AT4g04890/T1J1_3 mRNA, complete cds.
GenBank	AY062575	0.0	AY062575.1 Arabidopsis thaliana Unknown protein (At4g04890; T1J1.3) mRNA, complete cds.
GenBank	BT000144	0.0	BT000144.1 Arabidopsis thaliana Unknown protein (At4g04890) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010455798.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X1
Refseq	XP_010455799.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X1
Refseq	XP_010455800.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
Refseq	XP_010455802.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X3
Swissprot	Q93V99	0.0	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	R0FD46	0.0	R0FD46_9BRAS; Uncharacterized protein
STRING	XP_010455800.1	0.0	(Camelina sativa)

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

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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444]