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

Itr_sc000862.1_g00006.1

Organism

Ipomoea trifida

Taxonomic ID

35884

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea

Family

NF-YC

Protein Properties

Length: 142aa MW: 14844.1 Da PI: 10.6676

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Itr_sc000862.1_g00006.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	24.3	6.6e-08	31	105	19	93
NF-YC 19 helPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflv 93 ++P+ ri + lka + +++ aeaPv l+ e++ e+ + + a++nk++ + +i+ av + + l+ Itr_sc000862.1_g00006.1 31 LQFPVGRIARFLKAGKYAERVGAEAPVYLAVVLEYLAAEVLELAGNAARDNKKNRIVPRQIQLAVRNDEELSKLL 105 589***********************************999*******************99887665444 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00414	8.7E-72	10	130	IPR002119	Histone H2A
Gene3D	G3DSA:1.10.20.10	2.1E-59	14	129	IPR009072	Histone-fold
Pfam	PF00125	1.2E-13	18	96	IPR007125	Histone H2A/H2B/H3
CDD	cd00074	4.75E-64	20	127	No hit	No description
PRINTS	PR00620	4.7E-49	21	43	IPR002119	Histone H2A
SuperFamily	SSF47113	3.29E-41	24	127	IPR009072	Histone-fold
PRINTS	PR00620	4.7E-49	50	65	IPR002119	Histone H2A
PRINTS	PR00620	4.7E-49	65	78	IPR002119	Histone H2A
PRINTS	PR00620	4.7E-49	79	93	IPR002119	Histone H2A
Pfam	PF16211	8.0E-19	99	132	IPR032454	Histone H2A, C-terminal domain
PRINTS	PR00620	4.7E-49	107	125	IPR002119	Histone H2A

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000786	Cellular Component	nucleosome
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 142 aa Download sequence Send to blast
MSSGGGAGKG GAGRGKAKAT KSVSRSSKVG LQFPVGRIAR FLKAGKYAER VGAEAPVYLA 60 VVLEYLAAEV LELAGNAARD NKKNRIVPRQ IQLAVRNDEE LSKLLGDVTI ANGGVLPNIH 120 QTLLPKKAGS GKGEIDFASQ EF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1eqz_A	4e-57	7	134	2	127	PROTEIN (HISTONE H2A)
1eqz_E	4e-57	7	134	2	127	PROTEIN (HISTONE H2A)
1hq3_A	4e-57	7	134	2	127	HISTONE H2A-IV
1hq3_E	4e-57	7	134	2	127	HISTONE H2A-IV
1tzy_A	4e-57	7	134	2	127	Histone H2A-IV
1tzy_E	4e-57	7	134	2	127	Histone H2A-IV
2aro_A	4e-57	7	134	2	127	Histone H2A-IV
2aro_E	4e-57	7	134	2	127	Histone H2A-IV
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Functional Description ? help Back to Top
Source	Description
UniProt	Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation (By similarity). {ECO:0000250}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_020204559.1	6e-81	histone H2AX
Refseq	XP_028226627.1	6e-81	histone H2AX-like
Swissprot	Q9S9K7	1e-80	H2AXB_ARATH; Probable histone H2AXb
TrEMBL	A0A151R597	1e-79	A0A151R597_CAJCA; Histone H2A
TrEMBL	A0A445LGF9	3e-79	A0A445LGF9_GLYSO; Histone H2A (Fragment)
STRING	XP_008451417.1	2e-79	(Cucumis melo)
STRING	XP_004148883.1	2e-79	(Cucumis sativus)
STRING	XP_004171385.1	2e-79	(Cucumis sativus)
STRING	GLYMA19G42760.1	1e-79	(Glycine max)
STRING	XP_007147093.1	1e-79	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA164	6	9

Publications ? help Back to Top
Friesner JD,Liu B,Culligan K,Britt AB Ionizing radiation-dependent gamma-H2AX focus formation requires ataxia telangiectasia mutated and ataxia telangiectasia mutated and Rad3-related. Mol. Biol. Cell, 2005. 16(5): p. 2566-76 [PMID:15772150] Ebbs ML,Bender J Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell, 2006. 18(5): p. 1166-76 [PMID:16582009] Yi H,Sardesai N,Fujinuma T,Chan CW,Gelvin SB Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family members. Plant Cell, 2006. 18(7): p. 1575-89 [PMID:16751347] Sanchez-Moran E,Santos JL,Jones GH,Franklin FC ASY1 mediates AtDMC1-dependent interhomolog recombination during meiosis in Arabidopsis. Genes Dev., 2007. 21(17): p. 2220-33 [PMID:17785529] Charbonnel C,Gallego ME,White CI Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants. Plant J., 2010. 64(2): p. 280-90 [PMID:21070408] Lang J, et al. Plant γH2AX foci are required for proper DNA DSB repair responses and colocalize with E2F factors. New Phytol., 2012. 194(2): p. 353-63 [PMID:22339405] Qi Y,Zhang Y,Baller JA,Voytas DF Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants. Mutat. Res., 2016. 783: p. 9-14 [PMID:26687994] Ryu TH,Kim JK,Kim JI,Kim JH Transcriptome-based biological dosimetry of gamma radiation in Arabidopsis using DNA damage response genes. J Environ Radioact, 2018. 181: p. 94-101 [PMID:29128690] Lai J, et al. The Transcriptional Coactivator ADA2b Recruits a Structural Maintenance Protein to Double-Strand Breaks during DNA Repair in Plants. Plant Physiol., 2018. 176(4): p. 2613-2622 [PMID:29463775]