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

RrC4101_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

GRAS

Protein Properties

Length: 877aa MW: 96810.1 Da PI: 7.5548

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4101_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	411	1.1e-125	148	499	2	360
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNq 100 + L++cA+a+s++dl +a++++++l+ ++s +g+p++Rl ay++e+L a+la+s+s++yk+l+ +++ s+e l+++++++ev+P++kf+++ aN RrC4101_p1 148 RADLVSCAKAMSENDLMMARSMMEKLRLMVSVSGEPIERLGAYLLEGLVAQLASSGSSIYKSLNQCPEP--ASTELLSYMHILYEVCPYFKFGYMSANG 244 678**********************************************************766666..499********************* PP GRAS 101 aIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvk 197 aI ea+++e+rvHiiDf+i+qG QW++L+qa+a+Rp+gpp++RiTg+++ +s + l+ +g+rLak+A++++vpfefn v+ +++++++++L v+ RrC4101_p1 245 AIAEAMKEENRVHIIDFQIGQGSQWVTLIQAFAARPGGPPRIRITGIDDTTSAyaRGGGLSIVGNRLAKLAKQFKVPFEFNS-VSVSVSEVTPKNLGVR 342 *********************************************998899999********************.7999******** PP GRAS 198 pgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivn 296 pgEalaVn+++ lh+++desvs+e+ ++vkslsPkvv++veqe+++n++ F+ rf e+++yy a+f+s++++lpr++++ri+vE+++l+r++vn RrC4101_p1 343 PGEALAVNFAFVLHHMPDESVSTEN-----HRMVKSLSPKVVTLVEQESNTNTAAFFPRFKETMDYYDAMFESIDVTLPRNHKQRINVEQHCLARDVVN 436 *********************.....79*************************************************************** PP GRAS 297 vvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvl 360 ++acega+r+erhe l+kWr+r+++aGF+p+pls +++++++llr+++++ yr+ee++g+l+l RrC4101_p1 437 IIACEGADRVERHELLGKWRSRFGMAGFTPYPLSPLVNSTIRSLLRNYSDK-YRLEERDGALYL 499 *********************************************55.********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	68.882	121	494	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.7E-123	148	499	IPR005202	Transcription factor GRAS
Gene3D	G3DSA:2.160.20.10	3.4E-102	505	870	IPR012334	Pectin lyase fold
SuperFamily	SSF51126	3.46E-97	513	869	IPR011050	Pectin lyase fold/virulence factor
Pfam	PF00295	2.6E-108	527	855	IPR000743	Glycoside hydrolase, family 28
SMART	SM00710	35	650	676	IPR006626	Parallel beta-helix repeat
SMART	SM00710	740	677	698	IPR006626	Parallel beta-helix repeat
SMART	SM00710	9900	700	720	IPR006626	Parallel beta-helix repeat
PROSITE pattern	PS00502	0	707	720	IPR000743	Glycoside hydrolase, family 28
SMART	SM00710	3.5	730	751	IPR006626	Parallel beta-helix repeat
SMART	SM00710	2900	761	782	IPR006626	Parallel beta-helix repeat

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005975	Biological Process	carbohydrate metabolic process
GO:0004650	Molecular Function	polygalacturonase activity

Sequence ? help Back to Top
Protein Sequence Length: 877 aa Download sequence Send to blast
MCLVSDNFIF HLAHASGSHE MYKHPRQEIE DYSLPANSAG KRSRYVPVHN SRKRYCTPES 60 SSPDSPGYDV LSNARVLVSH NNSAYEDTSG SCVTDDFNDK IKELETVMMG PDSLDLVLDY 120 NDSFDSTLSQ ETNSWRSTLE AVSRRDLRAD LVSCAKAMSE NDLMMARSMM EKLRLMVSVS 180 GEPIERLGAY LLEGLVAQLA SSGSSIYKSL NQCPEPASTE LLSYMHILYE VCPYFKFGYM 240 SANGAIAEAM KEENRVHIID FQIGQGSQWV TLIQAFAARP GGPPRIRITG IDDTTSAYAR 300 GGGLSIVGNR LAKLAKQFKV PFEFNSVSVS VSEVTPKNLG VRPGEALAVN FAFVLHHMPD 360 ESVSTENHRM VKSLSPKVVT LVEQESNTNT AAFFPRFKET MDYYDAMFES IDVTLPRNHK 420 QRINVEQHCL ARDVVNIIAC EGADRVERHE LLGKWRSRFG MAGFTPYPLS PLVNSTIRSL 480 LRNYSDKYRL EERDGALYLA NAREFRITAR PGSDITGELS KLFKEACACV DRSTVLIPKG 540 EFRLGEIEMM GPCKAPIVIV LQGTVRADGN VNGKDYWIAF RRITNFRLNG GGIFDGEGNA 600 SWRANNCHKT SLTQCKRLPI SIRFDYITDG KVRDITSLDA KNFHINVIGA KNLTFEDVRI 660 IAPDESPNTD GIHVGRSDGI KIINTNIKTG DDCISVGDGM KNLLVEGVSC GPGHGISIGS 720 LGLYGHEEDV TGIRVVNCTL RNTDNGVRIK TWPSAACSTT ASGISFENIM LHNVSNPILI 780 DQEYCPWNRC NKNKPSTIKL VDIKFKNIRG TSGNKDAVKL LCSKAFPCKN VEIGDIDIKY 840 TGKDGPATFQ CCNISPKLVG KQCPKACSSP LTKAPGH

Sequence ? help Back to Top

Protein Sequence Length: 877 aa Download sequence Send to blast

MCLVSDNFIF HLAHASGSHE MYKHPRQEIE DYSLPANSAG KRSRYVPVHN SRKRYCTPES  60
SSPDSPGYDV LSNARVLVSH NNSAYEDTSG SCVTDDFNDK IKELETVMMG PDSLDLVLDY  120
NDSFDSTLSQ ETNSWRSTLE AVSRRDLRAD LVSCAKAMSE NDLMMARSMM EKLRLMVSVS  180
GEPIERLGAY LLEGLVAQLA SSGSSIYKSL NQCPEPASTE LLSYMHILYE VCPYFKFGYM  240
SANGAIAEAM KEENRVHIID FQIGQGSQWV TLIQAFAARP GGPPRIRITG IDDTTSAYAR  300
GGGLSIVGNR LAKLAKQFKV PFEFNSVSVS VSEVTPKNLG VRPGEALAVN FAFVLHHMPD  360
ESVSTENHRM VKSLSPKVVT LVEQESNTNT AAFFPRFKET MDYYDAMFES IDVTLPRNHK  420
QRINVEQHCL ARDVVNIIAC EGADRVERHE LLGKWRSRFG MAGFTPYPLS PLVNSTIRSL  480
LRNYSDKYRL EERDGALYLA NAREFRITAR PGSDITGELS KLFKEACACV DRSTVLIPKG  540
EFRLGEIEMM GPCKAPIVIV LQGTVRADGN VNGKDYWIAF RRITNFRLNG GGIFDGEGNA  600
SWRANNCHKT SLTQCKRLPI SIRFDYITDG KVRDITSLDA KNFHINVIGA KNLTFEDVRI  660
IAPDESPNTD GIHVGRSDGI KIINTNIKTG DDCISVGDGM KNLLVEGVSC GPGHGISIGS  720
LGLYGHEEDV TGIRVVNCTL RNTDNGVRIK TWPSAACSTT ASGISFENIM LHNVSNPILI  780
DQEYCPWNRC NKNKPSTIKL VDIKFKNIRG TSGNKDAVKL LCSKAFPCKN VEIGDIDIKY  840
TGKDGPATFQ CCNISPKLVG KQCPKACSSP LTKAPGH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5hyz_A	4e-58	151	489	8	348	GRAS family transcription factor containing protein, expressed
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in phytochrome A (phyA) signal transduction. {ECO:0000269\|PubMed:10817761}.

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	AF153443	0.0	AF153443.1 Arabidopsis thaliana phytochrome A signal transduction 1 protein (PAT1) mRNA, complete cds.
GenBank	AK117483	0.0	AK117483.1 Arabidopsis thaliana At5g48150 mRNA for putative SCARECROW gene regulator, complete cds, clone: RAFL17-10-L05.
GenBank	AK317252	0.0	AK317252.1 Arabidopsis thaliana AT5G48150 mRNA, complete cds, clone: RAFL22-43-D17.
GenBank	AK317747	0.0	AK317747.1 Arabidopsis thaliana AT5G48150 mRNA, complete cds, clone: RAFL22-04-F15.
GenBank	BT025326	0.0	BT025326.1 Arabidopsis thaliana At5g48150 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018440830.1	0.0	PREDICTED: scarecrow-like transcription factor PAT1
Refseq	XP_018440831.1	0.0	PREDICTED: scarecrow-like transcription factor PAT1
Refseq	XP_018440832.1	0.0	PREDICTED: scarecrow-like transcription factor PAT1
Swissprot	Q9LDL7	0.0	PAT1_ARATH; Scarecrow-like transcription factor PAT1
TrEMBL	A0A3P5Z5D7	0.0	A0A3P5Z5D7_BRACM; Uncharacterized protein
STRING	Bra037509.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM350	2	2

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G48150.2	0.0	GRAS family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Heyman J, et al. The heterodimeric transcription factor complex ERF115-PAT1 grants regeneration competence. Nat Plants, 2016. 2(11): p. 16165 [PMID:27797356]