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

Carubv10018554m

Common Name

CARUB_v10018554mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 374aa MW: 41316.8 Da PI: 6.6318

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10018554m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	24.1	6.4e-08	194	235	9	55
HHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 9 ErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 Er+ R++iN+++ +L++llP++ +K + ++L +A++Y+ +Lq Carubv10018554m 194 ERKQRNDINKKMRTLQDLLPNC-----RKDDNKSMLGEAINYMTNLQ 235 9******************9.....89888899*******998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.41E-7	181	239	No hit	No description
PROSITE profile	PS50888	12.201	185	234	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.8E-5	191	240	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	9.68E-13	193	252	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	7.3E-6	194	235	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	7.5E-12	194	245	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 374 aa Download sequence Send to blast
LNDPQFMELV FENGQILAKG QRSDLSLLNP RTKSIMDLYE AEYNEDFLKS INNFGDTQVV 60 LQNHLVAAPD TNMLESDKHV DGSTLIETFK ASSSKRMTMN YFNRKKIEFL PPDEQSVVAE 120 RTVESSFDTS SAGFTEDSQG STYLSSVLVC LKIVFVSTQS LDEESDDGRP RVSERTRKAL 180 VKRKRNAEAC HSPERKQRND INKKMRTLQD LLPNCRKDDN KSMLGEAINY MTNLQLQVQM 240 MTMGNRFVTP STLLPLGTHY SQMGVAMGMG MQMGAPQFLP GHILGAGLPG INNSANMLTF 300 LNHPGLAPMQ NSAPFTPTEK CSPQSVWPSY ATFPDQIPNP TFLSTLDGAT PYTRNHGTLT 360 DGGILSGKKS GNP*

Sequence ? help Back to Top

Protein Sequence Length: 374 aa Download sequence Send to blast

LNDPQFMELV FENGQILAKG QRSDLSLLNP RTKSIMDLYE AEYNEDFLKS INNFGDTQVV  60
LQNHLVAAPD TNMLESDKHV DGSTLIETFK ASSSKRMTMN YFNRKKIEFL PPDEQSVVAE  120
RTVESSFDTS SAGFTEDSQG STYLSSVLVC LKIVFVSTQS LDEESDDGRP RVSERTRKAL  180
VKRKRNAEAC HSPERKQRND INKKMRTLQD LLPNCRKDDN KSMLGEAINY MTNLQLQVQM  240
MTMGNRFVTP STLLPLGTHY SQMGVAMGMG MQMGAPQFLP GHILGAGLPG INNSANMLTF  300
LNHPGLAPMQ NSAPFTPTEK CSPQSVWPSY ATFPDQIPNP TFLSTLDGAT PYTRNHGTLT  360
DGGILSGKKS GNP*

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10018554m

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_023638997.1	0.0	LOW QUALITY PROTEIN: transcription factor PIF6
Swissprot	Q8L5W7	1e-176	PIF6_ARATH; Transcription factor PIF6
TrEMBL	R0HJ56	0.0	R0HJ56_9BRAS; Uncharacterized protein (Fragment)
STRING	XP_006292342.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13423	14	25

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G62090.2	1e-167	phytochrome interacting factor 3-like 2

Link Out ? help Back to Top
Phytozome	Carubv10018554m
Entrez Gene	17885547

Publications ? help Back to Top
Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Adams E,Diaz C,Hong JP,Shin R 14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs. Int J Mol Sci, 2014. 15(12): p. 22801-14 [PMID:25501334] Galvão VC,Collani S,Horrer D,Schmid M Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana. Plant J., 2015. 84(5): p. 949-62 [PMID:26466761] Gomez EJ,Gerhardt K,Judd J,Tabor JJ,Suh J Light-Activated Nuclear Translocation of Adeno-Associated Virus Nanoparticles Using Phytochrome B for Enhanced, Tunable, and Spatially Programmable Gene Delivery. ACS Nano, 2016. 10(1): p. 225-37 [PMID:26618393] Ochoa-Fernandez R, et al. Optogenetics in Plants: Red/Far-Red Light Control of Gene Expression. Methods Mol. Biol., 2016. 1408: p. 125-39 [PMID:26965120] Gangl R,Tenhaken R Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark. Front Plant Sci, 2016. 7: p. 1115 [PMID:27507985] Paik I,Kathare PK,Kim JI,Huq E Expanding Roles of PIFs in Signal Integration from Multiple Processes. Mol Plant, 2017. 10(8): p. 1035-1046 [PMID:28711729]