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_009144524.1

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

HB-other

Protein Properties

Length: 760aa MW: 84933.8 Da PI: 7.9236

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009144524.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	14.8	4.8e-05	686	746	1	54
TT--SS--HHHHHHHHHHHHHSSS-..-HHHHHHHHHHC.....TS-HHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknryp..saeereeLAkkl.....gLterqVkvWFqNrRak 54 +rkR ++++q+e +e++ ++ + sa+ +++ A+kl ++t q k+W NrRak XP_009144524.1 686 KRKRSIMSDDQVEMMEKAIVDEPDMrrSAAWIKKCAEKLnqngpRVTAMQLKNWLNNRRAK 746 79**************99866662266779**************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.1E-5	671	747	IPR009057	Homeodomain-like
PROSITE profile	PS50071	10.398	683	750	IPR001356	Homeobox domain
SMART	SM00389	0.003	685	754	IPR001356	Homeobox domain
CDD	cd00086	0.00456	686	749	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 760 aa Download sequence Send to blast
MKPPPKSSLR EALRETTLSK TRKSAICAHK IKRASTIDAD TAKHLIPAVN GLHWRDSLEI 60 HKLLQDNKDF CIYYNNVEKI SVEKLAVALP VHLLAVIKAH NRDDKFEYLL SGIRLLHTLC 120 ELTSRHSKLD QVLLDDCVLS AMMVDLVINA MVALGGNRKE SWKSDNESLV EATMVASTLH 180 LLHGFISPEF VDIVQVLLAH SKVDLFIETA FGAVHNVVRS LEAKLLYRGS DHPKKCPLKS 240 AKFHCQQAEA ALQFLHSLCQ EKLFSERVAK NKELCGKGGL LMLAKSILSL SVSPGFVKEA 300 TTVASMYRIK AKVLSLLHHI FEADSVSFLD ELERAGNLHL AQPIASEVLS LLKLGLSDSP 360 NDIASHEYPM GFVLLNAMRL AEVFSDDSNF QRFFTDHFST ILSALFCLSH EEFVSMLCSS 420 ALSSREDDAT LDYDLFKSAG WVLSVFSSSS LFDVPQFKLN FQNNLTMSSY ANQRTSLVIK 480 IMANLHCFAP DVCIEEDRNR FIKAFVSGLR KDPVSMPIQL PNSSYTPVAQ RATSVCRNIC 540 SLLRHADFLI TNGLDVKDLM MFRVFCKQLQ PLIRSEFEGS QATVKQRKEP LNLNIERASE 600 EPNVRVEGAA TKYNVNENME IVPRLKESDA DACNLETSSL DTRSNRGKSL VEDGDGDGDG 660 DVELAHELFK GSGSGEVKED EKQGKKRKRS IMSDDQVEMM EKAIVDEPDM RRSAAWIKKC 720 AEKLNQNGPR VTAMQLKNWL NNRRAKIARA MSGKTSKGKK

Sequence ? help Back to Top

Protein Sequence Length: 760 aa Download sequence Send to blast

MKPPPKSSLR EALRETTLSK TRKSAICAHK IKRASTIDAD TAKHLIPAVN GLHWRDSLEI  60
HKLLQDNKDF CIYYNNVEKI SVEKLAVALP VHLLAVIKAH NRDDKFEYLL SGIRLLHTLC  120
ELTSRHSKLD QVLLDDCVLS AMMVDLVINA MVALGGNRKE SWKSDNESLV EATMVASTLH  180
LLHGFISPEF VDIVQVLLAH SKVDLFIETA FGAVHNVVRS LEAKLLYRGS DHPKKCPLKS  240
AKFHCQQAEA ALQFLHSLCQ EKLFSERVAK NKELCGKGGL LMLAKSILSL SVSPGFVKEA  300
TTVASMYRIK AKVLSLLHHI FEADSVSFLD ELERAGNLHL AQPIASEVLS LLKLGLSDSP  360
NDIASHEYPM GFVLLNAMRL AEVFSDDSNF QRFFTDHFST ILSALFCLSH EEFVSMLCSS  420
ALSSREDDAT LDYDLFKSAG WVLSVFSSSS LFDVPQFKLN FQNNLTMSSY ANQRTSLVIK  480
IMANLHCFAP DVCIEEDRNR FIKAFVSGLR KDPVSMPIQL PNSSYTPVAQ RATSVCRNIC  540
SLLRHADFLI TNGLDVKDLM MFRVFCKQLQ PLIRSEFEGS QATVKQRKEP LNLNIERASE  600
EPNVRVEGAA TKYNVNENME IVPRLKESDA DACNLETSSL DTRSNRGKSL VEDGDGDGDG  660
DVELAHELFK GSGSGEVKED EKQGKKRKRS IMSDDQVEMM EKAIVDEPDM RRSAAWIKKC  720
AEKLNQNGPR VTAMQLKNWL NNRRAKIARA MSGKTSKGKK

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	684	689	KKRKRS

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed predominantly in dividing tissues such as young leaves, root tips, flower buds and embryos. {ECO:0000269\|PubMed:23641115}.

Functional Description ? help Back to Top
Source	Description
UniProt	Regulates COOLAIR, a set of antisense transcripts originating from the 3' end of FLOWERING LOCUS C (FLC). Associates with single-stranded DNA that is part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. R-loop stabilization mediated by NDX inhibits COOLAIR transcription, which in turn modifies FLC expression. {ECO:0000269\|PubMed:23641115}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009144524.1

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_009144524.1	0.0	PREDICTED: nodulin homeobox-like
Swissprot	F4JI44	0.0	NDX_ARATH; Nodulin homeobox
TrEMBL	A0A398AJS9	0.0	A0A398AJS9_BRACM; Uncharacterized protein
STRING	Bo2g103290.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8179	6	7

Publications ? help Back to Top
Mukherjee K,Brocchieri L,Bürglin TR A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol. Biol. Evol., 2009. 26(12): p. 2775-94 [PMID:19734295]