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

Gorai.011G016200.1

Common Name

B456_011G016200, LOC105778024

Organism

Gossypium raimondii

Taxonomic ID

29730

Taxonomic Lineage

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

Family

HD-ZIP

Protein Properties

Length: 735aa MW: 80762.2 Da PI: 5.8929

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.011G016200.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	61.8	1e-19	66	121	1	56
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 r++ +++t+ q++e+e+lF+++++p+ ++r++L+++lgL+ qVk+WFqN+R++ k Gorai.011G016200.1 66 RKRYHRHTQRQIQEMEALFKECPHPDDKQRKQLSRELGLDPLQVKFWFQNKRTQLK 121 789999**********************************************9877 PP
2	START	206.8	8.6e-65	254	476	1	206
HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS.........SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S... CS START 1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv........dsgealrasgvvdmvlallveellddkeqWdetla... 77 ela +a++el+++a+++ep+Wv++ + +n+ e+l++f+++ + +++ea+r+ ++ +m++++lve+l+d++ qW++ + Gorai.011G016200.1 254 ELAVTAMEELIRMAQSGEPLWVTDEnsiDVLNENEYLRIFPRGIGskpfanlgFRSEASREAALIIMNPVNLVEILMDVN-QWSRVFCgiv 343 57899*******************99**********999*******************************.**9999 PP .EEEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTC CS START 78 .kaetlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksng 160 +a+tl+v+s+g galq+m+ae+q++splvp R+ +f+Ry++++ +g w++vdvS+d+ ++ p + R++++pSg+li++++ng Gorai.011G016200.1 344 sRAMTLDVLSTGiagnynGALQVMTAEFQLPSPLVPtRENYFARYCKRHHDGIWAVVDVSLDNLRHAP----FTRCRRRPSGCLIQELPNG 430 9*************************************************************99....9************** PP EEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 161 hskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206 +skv+wve+v++++r ++ +++ lv+++la+gak+wvatl+rqce+ Gorai.011G016200.1 431 YSKVIWVENVEVDDRGVSDIYKTLVNTSLAFGAKRWVATLDRQCER 476 ******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	6.8E-22	46	121	IPR009057	Homeodomain-like
SuperFamily	SSF46689	5.01E-19	50	123	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.811	63	123	IPR001356	Homeobox domain
SMART	SM00389	6.0E-18	64	127	IPR001356	Homeobox domain
CDD	cd00086	1.01E-17	65	123	No hit	No description
Pfam	PF00046	2.5E-17	66	121	IPR001356	Homeobox domain
PROSITE pattern	PS00027	0	98	121	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	44.549	245	479	IPR002913	START domain
SuperFamily	SSF55961	2.06E-33	246	478	No hit	No description
CDD	cd08875	1.10E-119	249	475	No hit	No description
SMART	SM00234	3.7E-65	254	476	IPR002913	START domain
Pfam	PF01852	2.2E-55	255	476	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	4.4E-6	352	476	IPR023393	START-like domain
SuperFamily	SSF55961	5.22E-22	498	725	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: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: 735 aa Download sequence Send to blast
MFNSDLYENL NMFDMFQRPS DSDQTERNGD DDNNDTKSGT EVDAPSADDD NQGPASSGPS 60 RRRAKRKRYH RHTQRQIQEM EALFKECPHP DDKQRKQLSR ELGLDPLQVK FWFQNKRTQL 120 KAQTERHENG LLKAENEKLR AENHRYKEAL NNTSCPTCGG PAALGEMSFE EQHLRLENAR 180 LREEIERISG VTAKYVGKPI GPSFSRFADR APISFGTQPE FLGEYGGPGG GGGLGEVLRP 240 VSVTNEADKP LIVELAVTAM EELIRMAQSG EPLWVTDENS IDVLNENEYL RIFPRGIGSK 300 PFANLGFRSE ASREAALIIM NPVNLVEILM DVNQWSRVFC GIVSRAMTLD VLSTGIAGNY 360 NGALQVMTAE FQLPSPLVPT RENYFARYCK RHHDGIWAVV DVSLDNLRHA PFTRCRRRPS 420 GCLIQELPNG YSKVIWVENV EVDDRGVSDI YKTLVNTSLA FGAKRWVATL DRQCERLASA 480 MANSIPAGDL GVLNSSDGRK SILKLAERMV NSFCTGVGAS TAHAWTTLTG SDEIRVMTRK 540 SIDDPGRPPG IVLSAATSFW VAVPPRKAFN ILRSEKFRSE WDILSNGGVV DEMAHIANGR 600 DPGNCVSLLR VNSANASQSN MLILQESSND ATGSYVIYAP VDFAAMNIVL TGGDPDYVAL 660 LPSGFAILPD CEGPNRGIKI TEIGSGGSLV TLAFQILVDS APNSKISVGS VATVNSLIKC 720 TLERIRTAVM CNDA*

Sequence ? help Back to Top

Protein Sequence Length: 735 aa Download sequence Send to blast

MFNSDLYENL NMFDMFQRPS DSDQTERNGD DDNNDTKSGT EVDAPSADDD NQGPASSGPS  60
RRRAKRKRYH RHTQRQIQEM EALFKECPHP DDKQRKQLSR ELGLDPLQVK FWFQNKRTQL  120
KAQTERHENG LLKAENEKLR AENHRYKEAL NNTSCPTCGG PAALGEMSFE EQHLRLENAR  180
LREEIERISG VTAKYVGKPI GPSFSRFADR APISFGTQPE FLGEYGGPGG GGGLGEVLRP  240
VSVTNEADKP LIVELAVTAM EELIRMAQSG EPLWVTDENS IDVLNENEYL RIFPRGIGSK  300
PFANLGFRSE ASREAALIIM NPVNLVEILM DVNQWSRVFC GIVSRAMTLD VLSTGIAGNY  360
NGALQVMTAE FQLPSPLVPT RENYFARYCK RHHDGIWAVV DVSLDNLRHA PFTRCRRRPS  420
GCLIQELPNG YSKVIWVENV EVDDRGVSDI YKTLVNTSLA FGAKRWVATL DRQCERLASA  480
MANSIPAGDL GVLNSSDGRK SILKLAERMV NSFCTGVGAS TAHAWTTLTG SDEIRVMTRK  540
SIDDPGRPPG IVLSAATSFW VAVPPRKAFN ILRSEKFRSE WDILSNGGVV DEMAHIANGR  600
DPGNCVSLLR VNSANASQSN MLILQESSND ATGSYVIYAP VDFAAMNIVL TGGDPDYVAL  660
LPSGFAILPD CEGPNRGIKI TEIGSGGSLV TLAFQILVDS APNSKISVGS VATVNSLIKC  720
TLERIRTAVM CNDA*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	60	66	RRRAKRK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot meristems. {ECO:0000269\|PubMed:12505995}.

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	JX615980	1e-179	JX615980.1 Gossypium hirsutum clone NBRI_GE60293 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012457027.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2-like
Refseq	XP_012457028.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2-like
Refseq	XP_012457029.1	0.0	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2-like
Swissprot	Q93V99	0.0	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	A0A0D2RFF7	0.0	A0A0D2RFF7_GOSRA; Uncharacterized protein
STRING	Gorai.011G016200.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM24824	3	4

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	Gorai.011G016200.1
Entrez Gene	105778024

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] Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444]