PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

YABBY

Protein Properties

Length: 181aa MW: 20064 Da PI: 4.9374

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g030283m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	22.9	2.6e-07	20	90	85	157
YABBY 85 nvekeesastsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaa 157 n+ k +++ ++ kl++ ++++ +r +++ + P+k +r Psa+ f+ e + k +nP+++ a aa orange1.1g030283m 20 NDRKV--GKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAA 90 44433..3455566679999999999999******************999999******9999998877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47095	5.11E-26	41	125	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	4.3E-25	53	127	IPR009071	High mobility group box domain
SMART	SM00398	8.9E-25	54	125	IPR009071	High mobility group box domain
Pfam	PF00505	2.9E-24	55	124	IPR009071	High mobility group box domain
PROSITE profile	PS50118	19.558	55	124	IPR009071	High mobility group box domain
CDD	cd00084	9.13E-15	55	120	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 181 aa Download sequence Send to blast
MKGAKGKGAA RVSQEALKPN DRKVGKRKAA TAKLDSGSKR QGKREKKAKK DPNKPKRPPS 60 AFFVFLEEFR KTFKKENPNV TAVSAVGKAA GGKWKSMSPA EKAPYESKAE KLKSEYGKKM 120 NAYNKKQDGD EASDKSKSEV NDEDEASGEE EHQLEPEPEP EQDEDEEVEE DEDDEEDDDD 180 *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1j3c_A	1e-15	49	126	3	79	High mobility group protein 2
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.10067	0.0	callus

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in cotyledons, roots, stems, leaves and flowers (excluding pedicels). {ECO:0000269\|PubMed:17169924, ECO:0000269\|PubMed:17316617, ECO:0000269\|PubMed:9461286}.

Functional Description ? help Back to Top
Source	Description
UniProt	Binds preferentially double-stranded DNA. Modulates general plant growth and stress tolerance. Confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. {ECO:0000269\|PubMed:17114349, ECO:0000269\|PubMed:9461286}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by salt stress. {ECO:0000269\|PubMed:17169924}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006429363.1	1e-98	high mobility group B protein 1
Refseq	XP_006429364.1	1e-98	high mobility group B protein 1
Refseq	XP_006481020.1	2e-98	high mobility group B protein 1-like
Refseq	XP_006481021.1	2e-98	high mobility group B protein 1-like
Swissprot	O49595	2e-58	HMGB1_ARATH; High mobility group B protein 1
TrEMBL	A0A067E936	1e-121	A0A067E936_CITSI; Uncharacterized protein
STRING	XP_006481020.1	6e-98	(Citrus sinensis)
STRING	XP_006429363.1	5e-98	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6406	2	2

Link Out ? help Back to Top
Phytozome	orange1.1g030283m

Publications ? help Back to Top
Comella P, et al. Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III. Plant Mol. Biol., 1999. 41(5): p. 687-700 [PMID:10645728] Stemmer C,Leeming DJ,Franssen L,Grimm R,Grasser KD Phosphorylation of maize and Arabidopsis HMGB proteins by protein kinase CK2alpha. Biochemistry, 2003. 42(12): p. 3503-8 [PMID:12653554] Elo A,Lyznik A,Gonzalez DO,Kachman SD,Mackenzie SA Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome. Plant Cell, 2003. 15(7): p. 1619-31 [PMID:12837951] Launholt D,Merkle T,Houben A,Schulz A,Grasser KD Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus. Plant Cell, 2006. 18(11): p. 2904-18 [PMID:17114349] Kwak KJ,Kim JY,Kim YO,Kang H Characterization of transgenic Arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress. Plant Cell Physiol., 2007. 48(2): p. 221-31 [PMID:17169924] Launholt D,Grønlund JT,Nielsen HK,Grasser KD Overlapping expression patterns among the genes encoding Arabidopsis chromosomal high mobility group (HMG) proteins. FEBS Lett., 2007. 581(6): p. 1114-8 [PMID:17316617] Lildballe DL, et al. The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis. J. Mol. Biol., 2008. 384(1): p. 9-21 [PMID:18822296] Pedersen DS,Grasser KD The role of chromosomal HMGB proteins in plants. Biochim. Biophys. Acta, 2010 Jan-Feb. 1799(1-2): p. 171-4 [PMID:20123078] Pedersen DS, et al. Nucleocytoplasmic distribution of the Arabidopsis chromatin-associated HMGB2/3 and HMGB4 proteins. Plant Physiol., 2010. 154(4): p. 1831-41 [PMID:20940346] Schrumpfová PP,Fojtová M,Mokroš P,Grasser KD,Fajkus J Role of HMGB proteins in chromatin dynamics and telomere maintenance in Arabidopsis thaliana. Curr. Protein Pept. Sci., 2011. 12(2): p. 105-11 [PMID:21348847] Merkle T,Grasser KD Unexpected mobility of plant chromatin-associated HMGB proteins. Plant Signal Behav, 2011. 6(6): p. 878-80 [PMID:21543902] Li MW,Zhou L,Lam HM Paraformaldehyde Fixation May Lead to Misinterpretation of the Subcellular Localization of Plant High Mobility Group Box Proteins. PLoS ONE, 2015. 10(8): p. e0135033 [PMID:26270959] Roy A, et al. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Mol. Biol., 2016. 92(3): p. 371-88 [PMID:27503561] Stemmer C,Ritt C,Igloi GL,Grimm R,Grasser KD Variability in Arabidopsis thaliana chromosomal high-mobility-group-1-like proteins. Eur. J. Biochem., 1997. 250(3): p. 646-52 [PMID:9461286]