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.009G107500.1

Common Name

B456_009G107500, LOC105768079

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: 844aa MW: 92307 Da PI: 6.1799

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.009G107500.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	57.2	2.9e-18	26	83	4	57
-SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS Homeobox 4 RttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 ++t+eq+e+Le++++++++ps +r++L +++ +++ +q+kvWFqNrR +ek+ Gorai.009G107500.1 26 YVRYTAEQVEALERVYAECPKPSSLRRQQLIRECpilsNIEPKQIKVWFQNRRCREKQ 83 5789****************************************************97 PP
2	START	160.2	1.6e-50	164	371	2	204
HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EE CS START 2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..ga 90 +aee+++e+++ka+ ++ Wv+++ +++g++++ +f+ s+++sg a+ra+g+v +++ +e+l+d++ W+++++ e+ g g+ Gorai.009G107500.1 164 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFTISQSCSGVAARACGLVSLEPV-KIAEILKDRPSWSRDCRNLEVFTMFPAGngGT 253 7899****************************************************.7777777777***9999999998888 PP EEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXX CS START 91 lqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlp 177 ++l +a++ a+++l+p Rdf+++Ry+ +l+ g++v++++S++ p+ +++vRae+lpSg+li+p+++g+s +++v+h +l+++++ Gorai.009G107500.1 254 IELVYAQTFAPTTLAPaRDFWTLRYTTTLENGSLVVCERSLSGSGAGPSaaaAAQFVRAEVLPSGYLIRPCEGGGSIIHIVDHLNLEAWSV 344 ****************************************99999988999********************************** PP HHHHHHHHHHHHHHHHHHHHHHTXXXX CS START 178 hwllrslvksglaegaktwvatlqrqc 204 +++lr+l++s+ + ++k++ a+l++ + Gorai.009G107500.1 345 PEVLRPLYESSKVIAQKMTIAALRYIR 371 ********************99865 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00389	2.2E-15	22	88	IPR001356	Homeobox domain
SuperFamily	SSF46689	5.56E-16	23	86	IPR009057	Homeodomain-like
CDD	cd00086	3.63E-16	25	85	No hit	No description
Pfam	PF00046	7.5E-16	26	83	IPR001356	Homeobox domain
Gene3D	G3DSA:1.10.10.60	2.6E-18	27	84	IPR009057	Homeodomain-like
PROSITE profile	PS50071	15.127	28	84	IPR001356	Homeobox domain
CDD	cd14686	1.46E-6	77	116	No hit	No description
PROSITE profile	PS50848	27.593	154	382	IPR002913	START domain
CDD	cd08875	1.26E-65	158	374	No hit	No description
Gene3D	G3DSA:3.30.530.20	5.3E-19	163	367	IPR023393	START-like domain
SMART	SM00234	3.7E-41	163	373	IPR002913	START domain
SuperFamily	SSF55961	1.79E-32	163	375	No hit	No description
Pfam	PF01852	6.9E-48	164	371	IPR002913	START domain
Pfam	PF08670	1.1E-49	699	842	IPR013978	MEKHLA

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0008289	Molecular Function	lipid binding

Sequence ? help Back to Top
Protein Sequence Length: 844 aa Download sequence Send to blast
MAMALAQHRE SSSDSSINKH LDGGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECP 60 ILSNIEPKQI KVWFQNRRCR EKQKKESSRL QTVNRKLTAM NKLLMEENDR LQKQVSQMVC 120 ENGYMKQQLH TVNTSAADAN CDSLGTTPQH SLRDTNSPAG LLSIAEETLA EFLSKATGTA 180 VDWVQMPGMK PGPDSVGIFT ISQSCSGVAA RACGLVSLEP VKIAEILKDR PSWSRDCRNL 240 EVFTMFPAGN GGTIELVYAQ TFAPTTLAPA RDFWTLRYTT TLENGSLVVC ERSLSGSGAG 300 PSAAAAAQFV RAEVLPSGYL IRPCEGGGSI IHIVDHLNLE AWSVPEVLRP LYESSKVIAQ 360 KMTIAALRYI RQIAQETSGE VVYSLGRQPA VLRTFSQRLS RGFNDAINGF NDDGWSIMNC 420 DGTEDVIIAI NSIKSFSSTS NPANALSFLG GVLCAKASML LQNIAPAVLV RFLREHRSEW 480 ADFNVDAYCA ASLKAGTNAY PGMRPTRFTG SQIIMPLGHT IEHEELLEVI RLEGHSFVQE 540 DAFVSRDIHL LQICSGIDEN AVGACSELVF APIDEMFPDD APLLPSGFRV IPLDSKSSDT 600 QDSLTTNRTL DLTSSLEVGP ATNHAAGDTS SCRNTRSVLT IAFQFPFESN LRDNVATMAR 660 QYVRSVISSV QRVAMAISPS GLNPAVGSKL SPGSPEALTL AHWICRSYSY HLGAELLRSE 720 SLGGDSILKN LWQHQDAILC CSLKSQPVFI FANQAGLDML ETTLVALQDI TLDKLFDESG 780 RKALCSDFGK LMQQGYACLP AGICMSTMGR HVSYEQAFAW KVLEADESTV HCLAFSFVNW 840 SFV*

Sequence ? help Back to Top

Protein Sequence Length: 844 aa Download sequence Send to blast

MAMALAQHRE SSSDSSINKH LDGGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECP  60
ILSNIEPKQI KVWFQNRRCR EKQKKESSRL QTVNRKLTAM NKLLMEENDR LQKQVSQMVC  120
ENGYMKQQLH TVNTSAADAN CDSLGTTPQH SLRDTNSPAG LLSIAEETLA EFLSKATGTA  180
VDWVQMPGMK PGPDSVGIFT ISQSCSGVAA RACGLVSLEP VKIAEILKDR PSWSRDCRNL  240
EVFTMFPAGN GGTIELVYAQ TFAPTTLAPA RDFWTLRYTT TLENGSLVVC ERSLSGSGAG  300
PSAAAAAQFV RAEVLPSGYL IRPCEGGGSI IHIVDHLNLE AWSVPEVLRP LYESSKVIAQ  360
KMTIAALRYI RQIAQETSGE VVYSLGRQPA VLRTFSQRLS RGFNDAINGF NDDGWSIMNC  420
DGTEDVIIAI NSIKSFSSTS NPANALSFLG GVLCAKASML LQNIAPAVLV RFLREHRSEW  480
ADFNVDAYCA ASLKAGTNAY PGMRPTRFTG SQIIMPLGHT IEHEELLEVI RLEGHSFVQE  540
DAFVSRDIHL LQICSGIDEN AVGACSELVF APIDEMFPDD APLLPSGFRV IPLDSKSSDT  600
QDSLTTNRTL DLTSSLEVGP ATNHAAGDTS SCRNTRSVLT IAFQFPFESN LRDNVATMAR  660
QYVRSVISSV QRVAMAISPS GLNPAVGSKL SPGSPEALTL AHWICRSYSY HLGAELLRSE  720
SLGGDSILKN LWQHQDAILC CSLKSQPVFI FANQAGLDML ETTLVALQDI TLDKLFDESG  780
RKALCSDFGK LMQQGYACLP AGICMSTMGR HVSYEQAFAW KVLEADESTV HCLAFSFVNW  840
SFV*

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed at the earliest stages and throughout LSM initiation and development. In embryo development, expressed at the heart stage until the 'walking stick' stage in the adaxial portion of the cotyledon primordia, the shoot apical meristem (SAM) and the vascular precursor cells of the hypocotyl and root. In developing flowers, expressed first at stage 1 in the center of L3 layer and then expands to the center of L2 and L1 layers. Expressed in the center of flower meristem through stages 4 and 5. At stage 6, expressed in the adaxial side of the carpel primordia and then on the adaxial carpel face. {ECO:0000269\|PubMed:11169198}.
Uniprot	TISSUE SPECIFICITY: Expressed in the interfascicular regions of stem and vascular bundles of young roots and leaves. {ECO:0000269\|PubMed:10559440}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212). {ECO:0000269\|PubMed:10559440, ECO:0000269\|PubMed:11169198, ECO:0000269\|PubMed:11402186, ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:15598805, ECO:0000269\|PubMed:20807212, ECO:0000269\|PubMed:22781836, ECO:0000269\|PubMed:7555701}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. Repressed by ZPR and miR165. Induced by DOF5.1 (PubMed:20807212). {ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:17237362, ECO:0000269\|PubMed:20807212}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012443272.1	0.0	PREDICTED: homeobox-leucine zipper protein REVOLUTA-like
Swissprot	Q9SE43	0.0	REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBL	A0A0D2QDG5	0.0	A0A0D2QDG5_GOSRA; Uncharacterized protein
STRING	Gorai.009G107500.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4779	27	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G60690.1	0.0	HD-ZIP family protein

Link Out ? help Back to Top
Phytozome	Gorai.009G107500.1
Entrez Gene	105768079

Publications ? help Back to Top
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] Lian H,Li X,Liu Z,He Y HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis. J. Exp. Bot., 2013. 64(11): p. 3397-410 [PMID:23918970] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Baima S, et al. Negative feedback regulation of auxin signaling by ATHB8/ACL5-BUD2 transcription module. Mol Plant, 2014. 7(6): p. 1006-1025 [PMID:24777988] Jia X, et al. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. Plant Sci., 2015. 233: p. 11-21 [PMID:25711809] Roodbarkelari F,Du F,Truernit E,Laux T ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response. BMC Biol., 2015. 13: p. 74 [PMID:26358077] Shi B, et al. Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet., 2016. 12(7): p. e1006168 [PMID:27398935]