NDX_ARATH
ID NDX_ARATH Reviewed; 913 AA.
AC F4JI44; F4JI45; Q7GAL2; Q9ZTA5;
DT 14-OCT-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=Nodulin homeobox {ECO:0000303|PubMed:23641115};
DE AltName: Full=NDX1 homeobox protein homolog {ECO:0000303|PubMed:19734295};
DE Short=AtNDX1 {ECO:0000303|PubMed:19734295};
GN Name=NDX {ECO:0000303|PubMed:23641115};
GN OrderedLocusNames=At4g03090 {ECO:0000312|Araport:AT4G03090};
GN ORFNames=F4C21.1 {ECO:0000312|EMBL:AAD14437.1},
GN T4I9.3 {ECO:0000312|EMBL:AAC79096.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP IDENTIFICATION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=19734295; DOI=10.1093/molbev/msp201;
RA Mukherjee K., Brocchieri L., Buerglin T.R.;
RT "A comprehensive classification and evolutionary analysis of plant homeobox
RT genes.";
RL Mol. Biol. Evol. 26:2775-2794(2009).
RN [4]
RP FUNCTION, TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=23641115; DOI=10.1126/science.1234848;
RA Sun Q., Csorba T., Skourti-Stathaki K., Proudfoot N.J., Dean C.;
RT "R-loop stabilization represses antisense transcription at the Arabidopsis
RT FLC locus.";
RL Science 340:619-621(2013).
CC -!- FUNCTION: Regulates COOLAIR, a set of antisense transcripts originating
CC from the 3' end of FLOWERING LOCUS C (FLC). Associates with single-
CC stranded DNA that is part of an RNA-DNA hybrid, or R-loop, that covers
CC the COOLAIR promoter. R-loop stabilization mediated by NDX inhibits
CC COOLAIR transcription, which in turn modifies FLC expression.
CC {ECO:0000269|PubMed:23641115}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23641115}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:23641115}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage, Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4JI44-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JI44-2; Sequence=VSP_057909, VSP_057910;
CC -!- TISSUE SPECIFICITY: Expressed predominantly in dividing tissues such as
CC young leaves, root tips, flower buds and embryos.
CC {ECO:0000269|PubMed:23641115}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC79096.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAD14437.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB77794.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC005275; AAD14437.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AF069442; AAC79096.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161496; CAB77794.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82269.1; -; Genomic_DNA.
DR PIR; T01384; T01384.
DR RefSeq; NP_192218.5; NM_116543.6. [F4JI44-1]
DR AlphaFoldDB; F4JI44; -.
DR STRING; 3702.AT4G03090.1; -.
DR iPTMnet; F4JI44; -.
DR PaxDb; F4JI44; -.
DR PRIDE; F4JI44; -.
DR EnsemblPlants; AT4G03090.1; AT4G03090.1; AT4G03090. [F4JI44-1]
DR GeneID; 828094; -.
DR Gramene; AT4G03090.1; AT4G03090.1; AT4G03090. [F4JI44-1]
DR KEGG; ath:AT4G03090; -.
DR Araport; AT4G03090; -.
DR TAIR; locus:2139404; AT4G03090.
DR eggNOG; ENOG502QR3W; Eukaryota.
DR InParanoid; F4JI44; -.
DR OrthoDB; 142086at2759; -.
DR PRO; PR:F4JI44; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JI44; baseline and differential.
DR Genevisible; F4JI44; AT.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:TAIR.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:TAIR.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0060195; P:negative regulation of antisense RNA transcription; IDA:UniProtKB.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR GO; GO:0009845; P:seed germination; IMP:TAIR.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR039325; NDX.
DR PANTHER; PTHR35743; PTHR35743; 1.
DR SMART; SM00389; HOX; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
PE 2: Evidence at transcript level;
KW Alternative promoter usage; Alternative splicing; DNA-binding; Flowering;
KW Homeobox; Nucleus; Reference proteome.
FT CHAIN 1..913
FT /note="Nodulin homeobox"
FT /id="PRO_0000434148"
FT DNA_BIND 698..765
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 635..657
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 762..830
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 641..656
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 768..826
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..9
FT /note="Missing (in isoform 2)"
FT /id="VSP_057909"
FT VAR_SEQ 559..583
FT /note="Missing (in isoform 2)"
FT /id="VSP_057910"
SQ SEQUENCE 913 AA; 101566 MW; BA8EE74E8EA271A3 CRC64;
MVRLLQPKHM VQAVNALHWR NSVEFHKLLK DNGDFSICFN SEQVLPQKIS VEKMVKMLPR
HLIAVVMTPN KDGKSRYILC GIRLLQTLCD LTPRNAKLEQ VLLDDVKLSA QMIDLVILVI
IALGRNRKES CNSNKESLLE ATLVASCLHL FHGFISPNSQ DLVLVLLAHP RVDVFIDSAF
GAVLNVVISL KAKLLYRQTD SPKKLGASSV EEVNFHCQQA EAALQFLHSL CQHKPFRERV
AKNKELCGKG GVLRLAQSIL SLTITPEFVG ATVTIASTSR MKAKVLSILQ HLFEAESVSF
LDEVANAGNL HLAKTVASEV LKLLRLGLSK ASMATASPDY PMGFVLLNAM RLADVLTDDS
NFRSFFTEHF SMVLSAVFCL SHGDFLSMLC SSDLSSREDD ANVDYDLFKS AGWILSVFSS
SGQSVTPQFK LSLQNNLTMS SYAHQRTSLF IKMIANLHCF VPNVCQEQDR NRFIQNVMSG
LRKDPSSILI KMLPGSSYTP VAQRGTGVCR NLGSLLRHAE SLIPSSLNEE DFLLLRVFCD
QLQPLIHSEF EESQVQVKVK KLFALLYIGF TILWLICLVT LIQDIEGRGG NLSGKLKELL
NLNNEEASED CDVRVEGVMT KQGVNEEIDT VERLKESDAD ASNLETSGSD TSSNRGKGLV
EEGELVQNMS KRFKGSASGE VKEDEKSETF LVFEKQKKKR KRSIMNADQM GMIEKALAEE
PDLQRNSASR QLWADKISQK GSEVITSSQL KNWLNNRKAK LARANKQTGP AHDNNSSGDL
PESPGDENTW QQKPSTPIKD QTVTETPKTG ENLMRTSSSS EEGIKQGQQV RLMDERGDEI
GKGTVLRTDG EWNGLSLETR QICVVDVMEL SESYDGSKKM IPYGSDDVGR TFTEANSRFG
VMRVAWDVNK LQY
