PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

C2H2

Protein Properties

Length: 619aa MW: 65874.5 Da PI: 9.255

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.277240.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.1	3.2e-05	78	100	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Cucsa.277240.1 78 FICEVCNKGFQREQNLQLHRRGH 100 89*******************88 PP
2	zf-C2H2	12.4	0.00048	154	176	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k++ +s+ k H +t+ Cucsa.277240.1 154 WKCDKCSKRYAVQSDWKAHSKTC 176 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	7.0E-6	77	100	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.46E-7	77	100	No hit	No description
Pfam	PF12171	3.1E-5	78	100	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	78	100	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	78	100	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	80	100	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	119	149	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.3E-5	142	175	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.46E-7	149	174	No hit	No description
SMART	SM00355	140	154	174	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: 619 aa Download sequence Send to blast
MAASSSSVPL FGVREEGQMR GQQPPQPQPP PPSAPSNSST ALPTPPPQKK KRNQPGTPNP 60 DAEVIALSPK TLMATNRFIC EVCNKGFQRE QNLQLHRRGH NLPWKLKQKS TKEPKRKVYL 120 CPEPTCVHHD PSRALGDLTG IKKHYSRKHG EKKWKCDKCS KRYAVQSDWK AHSKTCGTRE 180 YRCDCGTLFS RRDSFITHRA FCDALAQESA RHPPNLGTAI GSHLYGGNSN VGLTLSQVPQ 240 MSSLQDHSNI TQSPHDVLRL GGGRTGQFTH LLPPSIGSSF RPPPQQAMPS SNAAFFGLSD 300 QTNQNSFHED HHQSQSQQGL FGNKPFHGLM QFPSDIQTHA NNNNNSASNL FNLSFISNPT 360 GDNTSNMNNN NDTNTNNSNS SSNNNNNLPS SLLNQFNGTN NGNNDGPASN IFAVNIMGDQ 420 INSAAVPSLY SNTAPGGCSS GTSGGGAIPH MSATALLQKA AQLGSTTSSS NTTATLLRTF 480 GSSSTSSGKA SDRTLFPPSY GGVVFGENES NLQDLMNSFA NASSGSGMFG SFGVESLEDP 540 TKLQQNLSTV SMGGGTDRLT RDFLGVGQIV RSMSGGGGGG GYTQREHKQG GQGIVMEGNE 600 SNTAPSSNAF GGGNGNYQ*

Sequence ? help Back to Top

Protein Sequence Length: 619 aa Download sequence Send to blast

MAASSSSVPL FGVREEGQMR GQQPPQPQPP PPSAPSNSST ALPTPPPQKK KRNQPGTPNP  60
DAEVIALSPK TLMATNRFIC EVCNKGFQRE QNLQLHRRGH NLPWKLKQKS TKEPKRKVYL  120
CPEPTCVHHD PSRALGDLTG IKKHYSRKHG EKKWKCDKCS KRYAVQSDWK AHSKTCGTRE  180
YRCDCGTLFS RRDSFITHRA FCDALAQESA RHPPNLGTAI GSHLYGGNSN VGLTLSQVPQ  240
MSSLQDHSNI TQSPHDVLRL GGGRTGQFTH LLPPSIGSSF RPPPQQAMPS SNAAFFGLSD  300
QTNQNSFHED HHQSQSQQGL FGNKPFHGLM QFPSDIQTHA NNNNNSASNL FNLSFISNPT  360
GDNTSNMNNN NDTNTNNSNS SSNNNNNLPS SLLNQFNGTN NGNNDGPASN IFAVNIMGDQ  420
INSAAVPSLY SNTAPGGCSS GTSGGGAIPH MSATALLQKA AQLGSTTSSS NTTATLLRTF  480
GSSSTSSGKA SDRTLFPPSY GGVVFGENES NLQDLMNSFA NASSGSGMFG SFGVESLEDP  540
TKLQQNLSTV SMGGGTDRLT RDFLGVGQIV RSMSGGGGGG GYTQREHKQG GQGIVMEGNE  600
SNTAPSSNAF GGGNGNYQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-34	150	211	3	64	Zinc finger protein JACKDAW
5b3h_F	3e-34	150	211	3	64	Zinc finger protein JACKDAW
Search in ModeBase

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00255	DAP	Transfer from AT2G02070	Download

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	LN681904	0.0	LN681904.1 Cucumis melo genomic scaffold, anchoredscaffold00053.
GenBank	LN713264	0.0	LN713264.1 Cucumis melo genomic chromosome, chr_10.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004140400.1	0.0	PREDICTED: protein indeterminate-domain 5, chloroplastic
Swissprot	Q9ZUL3	1e-144	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A0A0KMB9	0.0	A0A0A0KMB9_CUCSA; Uncharacterized protein
STRING	XP_004140400.1	0.0	(Cucumis sativus)
STRING	XP_004157851.1	0.0	(Cucumis sativus)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1536	33	97

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-117	indeterminate(ID)-domain 5

Link Out ? help Back to Top
Phytozome	Cucsa.277240.1
Entrez Gene	101219959

Publications ? help Back to Top
Ren Y, et al. An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE, 2009. 4(6): p. e5795 [PMID:19495411] Guo S, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384 [PMID:20565788] Li Z, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12: p. 540 [PMID:22047402] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]