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

PSME_00040628-RA

Organism

Pseudotsuga menziesii

Taxonomic ID

3357

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga

Family

NAC

Protein Properties

Length: 225aa MW: 25362.8 Da PI: 6.5107

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PSME_00040628-RA	genome	PRS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	25.5	3.7e-08	103	144	87	128
NAM 87 gkdkevlskkgelvglkktLvfykg.rapkgektdWvmheyrl 128 g++++v++ +ge++g+kk++v+ + + +k+ kt Wvm +y+l PSME_00040628-RA 103 GNTRKVYE-NGEQIGCKKIMVLNMAlKGKKPLKTIWVMYQYHL 144 889**9.999******9554777778*******98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
ProDom	PD315657	1.0E-4	6	40	IPR020529	Origin recognition complex, subunit 6, metazoa/plant
SuperFamily	SSF101941	2.09E-19	40	163	IPR003441	NAC domain
Pfam	PF02365	1.2E-5	49	144	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006260	Biological Process	DNA replication
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005664	Cellular Component	nuclear origin of replication recognition complex
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 225 aa Download sequence Send to blast
MDMEALGRKL GLAEKKTSIR KAEELRHLSN VHFDSSTFGV VAQDWPGLPT GVKFDPSEQQ 60 LLGHLAAKLG IGNARPHAFI NDFIKTMEED DGICYTHPEN LEGNTRKVYE NGEQIGCKKI 120 MVLNMALKGK KPLKTIWVMY QYHLGTEDNE KENEFVVSKI FYQQEKQCDK NNPGIPQEDA 180 GTSISKDDPL TPKTSTPPPP RSEKQHTCLD RIKEEHLFCA SLPQV

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor regulating the transcriptional activation response to gamma irradiation (PubMed:19549833). Required for stem-cell death induced by UVB or by gamma irradiation (PubMed:20634150). Not required for ATM activation, but participates in pathways governed by both ATM and ATR sensor kinases (PubMed:19549833). Involved in DNA damage response (DDR) system that regulates cell cycle arrest (PubMed:24399300). Functional homolog of animal p53 (PubMed:24736489). Regulates SMR5 and SMR7 transcription (PubMed:24399300). Regulates DNA repair and cytokinin signaling separately and plays a key role in controlling lateral root formation under genotoxic stress. {ECO:0000269\|PubMed:19549833, ECO:0000269\|PubMed:20634150, ECO:0000269\|PubMed:24399300, ECO:0000305\|PubMed:24736489}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not induced by zeocin or ionizing radiation treatment. {ECO:0000269\|PubMed:23907539}.

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	EF676620	8e-43	EF676620.1 Picea sitchensis clone WS02744_L04 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011627944.1	6e-56	SUPPRESSOR OF GAMMA RESPONSE 1 isoform X4
Refseq	XP_020531159.1	7e-56	SUPPRESSOR OF GAMMA RESPONSE 1 isoform X5
Swissprot	Q6NQK2	2e-41	NAC8_ARATH; SUPPRESSOR OF GAMMA RESPONSE 1
TrEMBL	B8LLI0	1e-74	B8LLI0_PICSI; Uncharacterized protein
STRING	ERM95816	5e-56	(Amborella trichopoda)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G25580.1	2e-40	NAC family protein

Publications ? help Back to Top
Yi D, et al. The Arabidopsis SIAMESE-RELATED cyclin-dependent kinase inhibitors SMR5 and SMR7 regulate the DNA damage checkpoint in response to reactive oxygen species. Plant Cell, 2014. 26(1): p. 296-309 [PMID:24399300] Biever JJ,Brinkman D,Gardner G UV-B inhibition of hypocotyl growth in etiolated Arabidopsis thaliana seedlings is a consequence of cell cycle arrest initiated by photodimer accumulation. J. Exp. Bot., 2014. 65(11): p. 2949-61 [PMID:24591052] Hu Z,Cools T,Kalhorzadeh P,Heyman J,De Veylder L Deficiency of the Arabidopsis helicase RTEL1 triggers a SOG1-dependent replication checkpoint in response to DNA cross-links. Plant Cell, 2015. 27(1): p. 149-61 [PMID:25595823] Chen P,Umeda M DNA double-strand breaks induce the expression of flavin-containing monooxygenase and reduce root meristem size in Arabidopsis thaliana. Genes Cells, 2015. 20(8): p. 636-46 [PMID:26033196] Sjogren CA,Bolaris SC,Larsen PB Aluminum-Dependent Terminal Differentiation of the Arabidopsis Root Tip Is Mediated through an ATR-, ALT2-, and SOG1-Regulated Transcriptional Response. Plant Cell, 2015. 27(9): p. 2501-15 [PMID:26320227] Yoshiyama KO SOG1: a master regulator of the DNA damage response in plants. Genes Genet. Syst., 2016. 90(4): p. 209-16 [PMID:26617076] Weimer AK, et al. The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis. EMBO J., 2016. 35(19): p. 2068-2086 [PMID:27497297] Davis OM,Ogita N,Inagaki S,Takahashi N,Umeda M DNA damage inhibits lateral root formation by up-regulating cytokinin biosynthesis genes in Arabidopsis thaliana. Genes Cells, 2016. 21(11): p. 1195-1208 [PMID:27658920] Pedroza-García JA, et al. Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis. Plant Physiol., 2017. 173(3): p. 1735-1749 [PMID:28153919] Horvath BM, et al. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO J., 2017. 36(9): p. 1261-1278 [PMID:28320736] Sjogren CA,Larsen PB SUV2, which encodes an ATR-related cell cycle checkpoint and putative plant ATRIP, is required for aluminium-dependent root growth inhibition in Arabidopsis. Plant Cell Environ., 2017. 40(9): p. 1849-1860 [PMID:28556304] Yoshiyama KO,Kaminoyama K,Sakamoto T,Kimura S Increased Phosphorylation of Ser-Gln Sites on SUPPRESSOR OF GAMMA RESPONSE1 Strengthens the DNA Damage Response in Arabidopsis thaliana. Plant Cell, 2017. 29(12): p. 3255-3268 [PMID:29208704] Johnson RA, et al. SUPPRESSOR OF GAMMA RESPONSE1 Links DNA Damage Response to Organ Regeneration. Plant Physiol., 2018. 176(2): p. 1665-1675 [PMID:29222192] Ogita N, et al. Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis. Plant J., 2018. 94(3): p. 439-453 [PMID:29430765] Cao X, et al. Roles of MSH2 and MSH6 in cadmium-induced G2/M checkpoint arrest in Arabidopsis roots. Chemosphere, 2018. 201: p. 586-594 [PMID:29533809]