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

Csa08g011330.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

ZF-HD

Protein Properties

Length: 379aa MW: 43481.9 Da PI: 10.2088

Description

ZF-HD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa08g011330.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	ZF-HD_dimer	74.6	1.5e-23	46	98	4	56
ZF-HD_dimer 4 vrYkeClkNhAaslGgh.avDGCgEfmpsegeegtaaalkCaACgCHRnFHRre 56 v+Y +ClkNh a++Gg ++DGCgEfm++ geegt++al C+ACgCHR+FH ++ Csa08g011330.1 46 VKYGKCLKNHMAHMGGRcSLDGCGEFMAA-GEEGTPEALSCSACGCHRSFHDKD 98 89************7369****9.999****************886 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
ProDom	PD125774	0.009	6	37	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
Pfam	PF04770	7.0E-6	8	37	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
ProDom	PD125774	4.0E-13	41	109	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
Pfam	PF04770	6.5E-22	46	97	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
TIGRFAMs	TIGR01566	1.1E-20	47	98	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
PROSITE profile	PS51523	20.582	48	98	IPR006456	ZF-HD homeobox protein, Cys/His-rich dimerisation domain
Gene3D	G3DSA:3.30.70.330	4.8E-27	151	265	IPR012677	Nucleotide-binding alpha-beta plait domain
SuperFamily	SSF54928	4.03E-26	181	286	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	17.506	184	262	IPR000504	RNA recognition motif domain
SMART	SM00360	4.3E-20	185	258	IPR000504	RNA recognition motif domain
Pfam	PF00076	2.5E-19	186	256	IPR000504	RNA recognition motif domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0016607	Cellular Component	nuclear speck
GO:0000166	Molecular Function	nucleotide binding
GO:0003676	Molecular Function	nucleic acid binding

Sequence ? help Back to Top
Protein Sequence Length: 379 aa Download sequence Send to blast
MCVNKINGEP KDHCRHFLAG GEEGTPEAFF CSGCGCHEID MSTAIVKYGK CLKNHMAHMG 60 GRCSLDGCGE FMAAGEEGTP EALSCSACGC HRSFHDKDYF VVDCILSPSK FHFLIHILAA 120 TERIGLGFVF DEISLEMARA RSRSRSYSPR PRHRSPPRDR KTTYDDNRHR ERLSSRDHES 180 SDPSGLLIHN LPLDARPNDL RDSFERFGPL KDIYLPRNYY TGEPRGFGFV KYRYAEDAAE 240 AMKRMNHKVI GGREITIVFA EENRKTPQEM RTTIHSSGRH GDYKRTSHRS PRHRYRSHSR 300 SRSPPRLDSR HSKAREDDLY SPPRSRSISR SPLPRKERKD KSYNVSQSPR RNRRSREEVL 360 TPIRSRSLSR SRSRSLSR*

Sequence ? help Back to Top

Protein Sequence Length: 379 aa Download sequence Send to blast

MCVNKINGEP KDHCRHFLAG GEEGTPEAFF CSGCGCHEID MSTAIVKYGK CLKNHMAHMG  60
GRCSLDGCGE FMAAGEEGTP EALSCSACGC HRSFHDKDYF VVDCILSPSK FHFLIHILAA  120
TERIGLGFVF DEISLEMARA RSRSRSYSPR PRHRSPPRDR KTTYDDNRHR ERLSSRDHES  180
SDPSGLLIHN LPLDARPNDL RDSFERFGPL KDIYLPRNYY TGEPRGFGFV KYRYAEDAAE  240
AMKRMNHKVI GGREITIVFA EENRKTPQEM RTTIHSSGRH GDYKRTSHRS PRHRYRSHSR  300
SRSPPRLDSR HSKAREDDLY SPPRSRSISR SPLPRKERKD KSYNVSQSPR RNRRSREEVL  360
TPIRSRSLSR SRSRSLSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2kn4_A	2e-12	184	264	71	151	Immunoglobulin G-binding protein G, Splicing factor; arginine/serine-rich 2
2lea_A	1e-12	186	264	50	128	Serine/arginine-rich splicing factor 2
2leb_A	1e-12	186	264	50	128	Serine/arginine-rich splicing factor 2
2lec_A	1e-12	186	264	50	128	Serine/arginine-rich splicing factor 2
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in intron recognition and spliceosome assembly (Probable). Probably active at the 5' splice sites. {ECO:0000305}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa08g011330.1

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	DQ446966	0.0	DQ446966.1 Arabidopsis thaliana clone pENTR221-At5g18810 28 kDa SC35-like splicing factor (At5g18810) mRNA, complete cds.
GenBank	DQ653294	0.0	DQ653294.1 Arabidopsis thaliana clone 0000019121_0000013167 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010420654.1	1e-168	PREDICTED: serine/arginine-rich SC35-like splicing factor SCL28
Swissprot	Q1PDV2	5e-82	SRC28_ARATH; Serine/arginine-rich SC35-like splicing factor SCL28
TrEMBL	R0H131	1e-103	R0H131_9BRAS; Uncharacterized protein
STRING	XP_010420654.1	1e-167	(Camelina sativa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02540.1	3e-18	homeobox protein 21

Publications ? help Back to Top
Lopato S, et al. Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors. J. Biol. Chem., 2002. 277(42): p. 39989-98 [PMID:12176998] Lorković ZJ,Hilscher J,Barta A Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells. Mol. Biol. Cell, 2004. 15(7): p. 3233-43 [PMID:15133128] Kalyna M,Barta A A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions? Biochem. Soc. Trans., 2004. 32(Pt 4): p. 561-4 [PMID:15270675] Gullerova M,Barta A,Lorkovic ZJ AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. RNA, 2006. 12(4): p. 631-43 [PMID:16497658] Iida K,Go M Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Mol. Biol. Evol., 2006. 23(5): p. 1085-94 [PMID:16520337] Tanabe N,Yoshimura K,Kimura A,Yabuta Y,Shigeoka S Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. Plant Cell Physiol., 2007. 48(7): p. 1036-49 [PMID:17556373] Lorković ZJ,Hilscher J,Barta A Co-localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nuclei. Exp. Cell Res., 2008. 314(17): p. 3175-86 [PMID:18674533] Barta A,Kalyna M,Reddy AS Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell, 2010. 22(9): p. 2926-9 [PMID:20884799] Richardson DN, et al. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PLoS ONE, 2011. 6(9): p. e24542 [PMID:21935421] Cruz TM,Carvalho RF,Richardson DN,Duque P Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression. Int J Mol Sci, 2014. 15(10): p. 17541-64 [PMID:25268622]