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.008G169000.3

Common Name

B456_008G169000

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

C2H2

Protein Properties

Length: 537aa MW: 58147.2 Da PI: 8.6073

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.008G169000.3	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.7e-05	24	46	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Gorai.008G169000.3 24 FICEVCNKGFQREQNLQLHRRGH 46 89*******************88 PP
2	zf-C2H2	13.3	0.00025	100	122	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Gorai.008G169000.3 100 WKCEKCSKRYAVQSDWKAHSKTC 122 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	5.9E-6	23	46	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.29E-7	23	46	No hit	No description
Pfam	PF12171	2.6E-5	24	46	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	24	46	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	24	46	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	26	46	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	65	95	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.9E-5	88	121	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.29E-7	95	120	No hit	No description
SMART	SM00355	130	100	120	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 537 aa Download sequence Send to blast
MMETDPDAEV VALSPKTLMA TNRFICEVCN KGFQREQNLQ LHRRGHNLPW KLKQKTTKEV 60 KKKVYLCPEP TCVHHDPSRA LGDLTGIKKH YSRKHGEKKW KCEKCSKRYA VQSDWKAHSK 120 TCGTREYRCD CGTLFSRRDS FITHRAFCDA LAQETARHPP PLNSIGTHLY GTSNYMGLGL 180 SQVGTQISSI QDPNNNQTAA DILKLGGGGA SRSSQFDHLL PPSMGCSSSS SFRPQQQAMG 240 FVMEESNQIF NQEHQSQHGL LGNSKPFQGL MQFPPDDNNN NNNNNASNAS SAANLFNLSF 300 LSNSGNNGGA GDYNLTSSGL LMSDNFNNEN GGNGGTNNAA NLFSNNLMSD QMTSNIPSLF 360 SSSVQNNDMV PQMSATALLQ KAAQMGSTSS NKNTNDDSLL RTFANSSSTG TKTSNFGAIF 420 GDTAGNNLHE LMNSIASGNS PIFGSGYDAV HGQESPYTNR SSMGQEQPPQ SMNVSGGGSD 480 RLTRDFLGVG QIVRNMRGGA AQQRQGIGIS RLSSERNSNI TAPTSQQSFG ERGNFQ*

Sequence ? help Back to Top

Protein Sequence Length: 537 aa Download sequence Send to blast

MMETDPDAEV VALSPKTLMA TNRFICEVCN KGFQREQNLQ LHRRGHNLPW KLKQKTTKEV  60
KKKVYLCPEP TCVHHDPSRA LGDLTGIKKH YSRKHGEKKW KCEKCSKRYA VQSDWKAHSK  120
TCGTREYRCD CGTLFSRRDS FITHRAFCDA LAQETARHPP PLNSIGTHLY GTSNYMGLGL  180
SQVGTQISSI QDPNNNQTAA DILKLGGGGA SRSSQFDHLL PPSMGCSSSS SFRPQQQAMG  240
FVMEESNQIF NQEHQSQHGL LGNSKPFQGL MQFPPDDNNN NNNNNASNAS SAANLFNLSF  300
LSNSGNNGGA GDYNLTSSGL LMSDNFNNEN GGNGGTNNAA NLFSNNLMSD QMTSNIPSLF  360
SSSVQNNDMV PQMSATALLQ KAAQMGSTSS NKNTNDDSLL RTFANSSSTG TKTSNFGAIF  420
GDTAGNNLHE LMNSIASGNS PIFGSGYDAV HGQESPYTNR SSMGQEQPPQ SMNVSGGGSD  480
RLTRDFLGVG QIVRNMRGGA AQQRQGIGIS RLSSERNSNI TAPTSQQSFG ERGNFQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-34	96	157	3	64	Zinc finger protein JACKDAW
5b3h_F	4e-34	96	157	3	64	Zinc finger protein JACKDAW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305\|PubMed:22898356}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:22898356, ECO:0000269\|PubMed:24821766}.

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	JX614606	1e-154	JX614606.1 Gossypium hirsutum clone NBRI_GE58125 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012438385.1	0.0	PREDICTED: protein indeterminate-domain 5, chloroplastic-like
Swissprot	Q9ZUL3	1e-138	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A0D2RGQ6	0.0	A0A0D2RGQ6_GOSRA; Uncharacterized protein
STRING	Gorai.008G169000.1	0.0	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-100	indeterminate(ID)-domain 5

Link Out ? help Back to Top
Phytozome	Gorai.008G169000.3

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] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]