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_009111142.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 399aa MW: 43865.7 Da PI: 7.7907

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009111142.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	30.7	5.4e-10	117	140	3	26
S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHg 26 e C+ f+r G C++G+ C FaHg XP_009111142.1 117 AEVCPEFRRDGDCSRGEECEFAHG 140 589********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF90229	9.03E-6	113	144	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.0E-5	114	141	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.526	114	142	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.2E-6	115	142	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.8E-8	117	140	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.343	150	174	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.7	150	173	IPR000571	Zinc finger, CCCH-type

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

Sequence ? help Back to Top
Protein Sequence Length: 399 aa Download sequence Send to blast
MDVVMRPTVD IPPRKLLLAE SSPRSSPRKH NWNNKVSNKI ATSEHEEDNE DGNNKETKEY 60 CYDSDTDDPY ASEHFRMFEF KIRRCTRSRS HDWTDCPFAH PGEKARRRDP RRFQYSAEVC 120 PEFRRDGDCS RGEECEFAHG VFECWLHPIR YRTEACKDGK HCKRKGCFFA HSPRQLRVLP 180 PENVSGGGSA SGSPAVAKNP CCMFCSSSPT STLLGNLSHL SRSPSLSPPL SPAHKAAAFS 240 RLRNRAASAV SEAVSAAAAA GSVNYNDVLN ELVNSLDSIN LAEALHVSSS SPVTTPVSAA 300 AAAFASSCGL SNQRLHLQQQ QSSPLQFALS PSTPSYLATS FSPSSPSYLT NSPRANIFSG 360 EITPRQRQKN EFTAVRDKTS FEDGSCGDPD LGWVNDLLT

Sequence ? help Back to Top

Protein Sequence Length: 399 aa Download sequence Send to blast

MDVVMRPTVD IPPRKLLLAE SSPRSSPRKH NWNNKVSNKI ATSEHEEDNE DGNNKETKEY  60
CYDSDTDDPY ASEHFRMFEF KIRRCTRSRS HDWTDCPFAH PGEKARRRDP RRFQYSAEVC  120
PEFRRDGDCS RGEECEFAHG VFECWLHPIR YRTEACKDGK HCKRKGCFFA HSPRQLRVLP  180
PENVSGGGSA SGSPAVAKNP CCMFCSSSPT STLLGNLSHL SRSPSLSPPL SPAHKAAAFS  240
RLRNRAASAV SEAVSAAAAA GSVNYNDVLN ELVNSLDSIN LAEALHVSSS SPVTTPVSAA  300
AAAFASSCGL SNQRLHLQQQ QSSPLQFALS PSTPSYLATS FSPSSPSYLT NSPRANIFSG  360
EITPRQRQKN EFTAVRDKTS FEDGSCGDPD LGWVNDLLT

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Specifically expressed in seeds. {ECO:0000269\|PubMed:18487351}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription repressor that functions as negative regulator of phytochrome-mediated promotion of seed germination. Inhibits seed germination by regulating the expression of gibberellic acid (GA) and abscisic acid (ABA) metabolic genes. Does not regulate the expression of the DELLA genes RGA and RGA1. Activated by PIL5, a phytochrome-interacting basic helix-loop-helix transcription factor. {ECO:0000269\|PubMed:18487351}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009111142.1

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_009111142.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 2
Swissprot	Q9ZWA1	0.0	C3H2_ARATH; Zinc finger CCCH domain-containing protein 2
TrEMBL	M4EP22	0.0	M4EP22_BRARP; Uncharacterized protein
STRING	Bra030542.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2987	27	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03790.1	1e-164	C3H family 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] Chang G, et al. AFP2 as the novel regulator breaks high-temperature-induced seeds secondary dormancy through ABI5 and SOM in Arabidopsis thaliana. Biochem. Biophys. Res. Commun., 2018. 501(1): p. 232-238 [PMID:29723526]