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

XP_013616622.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 440aa MW: 49353.7 Da PI: 8.9093

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013616622.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.6	1.1e-05	78	100	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y C++C++ F r nL+ H r+H XP_013616622.1 78 YICEICNQGFQRDQNLQMHRRRH 100 89********************9 PP
2	zf-C2H2	14.5	0.0001	156	178	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C+ C+k + +s++k H++t+ XP_013616622.1 156 WVCERCSKGYAVQSDYKAHLKTC 178 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	5.6E-5	75	101	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-5	77	100	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0065	78	100	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.866	78	100	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	80	100	IPR007087	Zinc finger, C2H2
SMART	SM00355	160	120	150	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.4E-4	147	177	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	100	156	183	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: 440 aa Download sequence Send to blast
MMRTDQDTVV MLDAASNKNT SNTCCVVSSS SSDPFLSSSE NVVATTNTSN QKRKRRPADP 60 DAEVVSLSPR TLLESDRYIC EICNQGFQRD QNLQMHRRRH KVPWKLLKRD NNIEVKKRVY 120 VCPEPTCLHH DPCHALGDLV GIKKHFRRKH SNHKQWVCER CSKGYAVQSD YKAHLKTCGT 180 RGHSCDCGRV FSRVESFIEH QDNCSIRKVH REPPPPPQAT VNVPACSSRT ASTTSTPSAE 240 TNYGGAVATP LPLEGRPIPI RNSSNDVNLE LQLLPLTPNQ NPNQENQQHK VKEPSHHRNH 300 HDTTNLNLSI APSAPSLSHQ YNNFDRIKEI MASEQIMKIA MKEKAYAEEA KREAKRQREI 360 AENEFVNAKK IRQQAQAELE RAKLLKEQSV KKISSTIMQV TCQICKGQFQ AVAVPAAASA 420 DETSLVVSYM SSVNTDGEAS

Sequence ? help Back to Top

Protein Sequence Length: 440 aa Download sequence Send to blast

MMRTDQDTVV MLDAASNKNT SNTCCVVSSS SSDPFLSSSE NVVATTNTSN QKRKRRPADP  60
DAEVVSLSPR TLLESDRYIC EICNQGFQRD QNLQMHRRRH KVPWKLLKRD NNIEVKKRVY  120
VCPEPTCLHH DPCHALGDLV GIKKHFRRKH SNHKQWVCER CSKGYAVQSD YKAHLKTCGT  180
RGHSCDCGRV FSRVESFIEH QDNCSIRKVH REPPPPPQAT VNVPACSSRT ASTTSTPSAE  240
TNYGGAVATP LPLEGRPIPI RNSSNDVNLE LQLLPLTPNQ NPNQENQQHK VKEPSHHRNH  300
HDTTNLNLSI APSAPSLSHQ YNNFDRIKEI MASEQIMKIA MKEKAYAEEA KREAKRQREI  360
AENEFVNAKK IRQQAQAELE RAKLLKEQSV KKISSTIMQV TCQICKGQFQ AVAVPAAASA  420
DETSLVVSYM SSVNTDGEAS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-16	154	204	5	55	Zinc finger protein JACKDAW
5b3h_F	1e-16	154	204	5	55	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269\|PubMed:16813575}.
Uniprot	TISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269\|PubMed:16813575}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269\|PubMed:16813575, ECO:0000269\|PubMed:18259878, ECO:0000269\|PubMed:24039602, ECO:0000269\|PubMed:9210330}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013616622.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by auxin. {ECO:0000269\|PubMed:24039602}.

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	AK226703	0.0	AK226703.1 Arabidopsis thaliana mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL07-61-I21.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013616622.1	0.0	PREDICTED: protein SHOOT GRAVITROPISM 5-like isoform X2
Swissprot	F4IPE3	0.0	IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBL	A0A3P6AWF4	0.0	A0A3P6AWF4_BRACM; Uncharacterized protein
STRING	Bra026624.1-P	0.0	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G01940.1	0.0	C2H2-like zinc finger protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Kim JY,Ryu JY,Baek K,Park CM High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. New Phytol., 2016. 209(1): p. 265-79 [PMID:26256266] Ryu JY,Kim JY,Park CM Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis. Plant Signal Behav, 2015. 10(11): p. e1093715 [PMID:26452406] Qu Y, et al. Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis. J. Exp. Bot., 2017. 68(17): p. 4851-4867 [PMID:28992128] Shi H, et al. Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17. J. Pineal Res., 2018. 65(2): p. e12494 [PMID:29607541]