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

Sobic.010G111800.2.p

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

NAC

Protein Properties

Length: 489aa MW: 55095.4 Da PI: 4.9186

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.010G111800.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	106.3	3.7e-33	92	230	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkk.....leleevikevd....iykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratk. 79 lp+G++F+P+d+el+++ L+k+ +++ +++ +i++v+ i++++P++Lp vk++ + +fF+++ k+y+tg+rk+r+++ Sobic.010G111800.2.p 92 LPKGVKFDPSDQELIWHLLAKHGKSDIkphpfIDE--FIPTVEedegICYTHPQKLP-GVKQNGSVSHFFHRTFKAYNTGTRKRRKINt 177 799**********98888765444344544222..2443322234******.667778899**************7554 PP NAM 80 ...sgyWkatgkdkevlskkgelvglkktLvfykg..rapkgektdWvmheyrl 128 + +W++tgk+k+vl +g++ g kk++v+y + k+ekt+Wvmh+y+l Sobic.010G111800.2.p 178 vdaDVRWHKTGKTKPVLL-DGKQLGSKKIMVLYMSpaKGGKAEKTNWVMHQYHL 230 566889********.999*******6522666778*******98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	3.14E-38	76	249	IPR003441	NAC domain
PROSITE profile	PS51005	31.984	92	249	IPR003441	NAC domain
Pfam	PF02365	2.0E-14	93	230	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000077	Biological Process	DNA damage checkpoint
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010332	Biological Process	response to gamma radiation
GO:0040020	Biological Process	regulation of meiotic nuclear division
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 489 aa Download sequence Send to blast
MPRRFFFFAV DGSSGQMMTF LYFGFNDKED MSTVRMKTTW IIDSQRFATK IKNASGSSDP 60 SKQKWISNPS KECPKCSHVI DNSDVVHHWP GLPKGVKFDP SDQELIWHLL AKHGKSDIKP 120 HPFIDEFIPT VEEDEGICYT HPQKLPGVKQ NGSVSHFFHR TFKAYNTGTR KRRKINTVDA 180 DVRWHKTGKT KPVLLDGKQL GSKKIMVLYM SPAKGGKAEK TNWVMHQYHL GIGEDERDGE 240 YVVSKLFFQQ QFKPGDKNAQ ELTTSDDLES IAAEADLTDF TTLPADKHVG TIQVVHNSEH 300 NLNQVTTSDD LESMAAEADL PDFTTLPADK HVGTIQEVQN PEHNLYQVNR NCEINIEETV 360 VLPPSEKTED GDNPQSQDPK LWEGDSQFEL LDSQQLAEGL ALCDEFLLSQ SQTSCGGGDE 420 PRVTKPCLAA YAHLSTEDFK KDLEECQRLE PTDNTNLELD STNEFRLSQI EFSQDSFTTW 480 AVGKMTDD*

Sequence ? help Back to Top

Protein Sequence Length: 489 aa Download sequence Send to blast

MPRRFFFFAV DGSSGQMMTF LYFGFNDKED MSTVRMKTTW IIDSQRFATK IKNASGSSDP  60
SKQKWISNPS KECPKCSHVI DNSDVVHHWP GLPKGVKFDP SDQELIWHLL AKHGKSDIKP  120
HPFIDEFIPT VEEDEGICYT HPQKLPGVKQ NGSVSHFFHR TFKAYNTGTR KRRKINTVDA  180
DVRWHKTGKT KPVLLDGKQL GSKKIMVLYM SPAKGGKAEK TNWVMHQYHL GIGEDERDGE  240
YVVSKLFFQQ QFKPGDKNAQ ELTTSDDLES IAAEADLTDF TTLPADKHVG TIQVVHNSEH  300
NLNQVTTSDD LESMAAEADL PDFTTLPADK HVGTIQEVQN PEHNLYQVNR NCEINIEETV  360
VLPPSEKTED GDNPQSQDPK LWEGDSQFEL LDSQQLAEGL ALCDEFLLSQ SQTSCGGGDE  420
PRVTKPCLAA YAHLSTEDFK KDLEECQRLE PTDNTNLELD STNEFRLSQI EFSQDSFTTW  480
AVGKMTDD*

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in shoot and root apical meristems, in lateral root primordia, in the vasculature of young leaves and in the root stele. {ECO:0000269\|PubMed:23907539}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.010G111800.2.p

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	BT055862	0.0	BT055862.1 Zea mays full-length cDNA clone ZM_BFb0341H11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002436832.1	0.0	SUPPRESSOR OF GAMMA RESPONSE 1
Swissprot	Q6NQK2	1e-147	NAC8_ARATH; SUPPRESSOR OF GAMMA RESPONSE 1
TrEMBL	A0A1W0VSI7	0.0	A0A1W0VSI7_SORBI; Uncharacterized protein
STRING	Sb10g009670.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6785	36	51
Representative plant	OGRP8264	10	16

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G25580.1	1e-150	NAC family protein

Link Out ? help Back to Top
Phytozome	Sobic.010G111800.2.p

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]