LXL04_025939 | RubberDandelionOmics

Gene overview

LXL04_025939

Reference: OH-1004 Chr: Chr05 Coordinates: 118757160-118759351 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1032 bp · LXL04_025939|LXL04_025939|OH1004|cDNA

ATGGAAGGAGAAGTGAACAAGGAGGCTGATAAACTTCCTCCAGGATTTCGGTTTCATCCAACTGATGAAGAACTCATCACTTCTTATCTTGTAAACAAGATATCAGATTCAAGTTTTACTGGAAGGGCAATAACTGATGTTGATCTCAATAAATGTGAGCCTTGGGATCTTCCTGGAAAGGcgaaaatgggagagaaagagtggtACTTCTTCAGCCTAAGAGACCGGAAATACCCAACAGGAGTGAGGACAAACAGAGC...

CDS

Download CDS FASTA

1032 bp · LXL04_025939|LXL04_025939|OH1004|CDS

ATGGAAGGAGAAGTGAACAAGGAGGCTGATAAACTTCCTCCAGGATTTCGGTTTCATCCAACTGATGAAGAACTCATCACTTCTTATCTTGTAAACAAGATATCAGATTCAAGTTTTACTGGAAGGGCAATAACTGATGTTGATCTCAATAAATGTGAGCCTTGGGATCTTCCTGGAAAGGCGAAAATGGGAGAGAAAGAGTGGTACTTCTTCAGCCTAAGAGACCGGAAATACCCAACAGGAGTGAGGACAAACAGAGC...

Protein

Download Protein FASTA

343 aa · LXL04_025939|LXL04_025939|OH1004|PROTEIN

MEGEVNKEADKLPPGFRFHPTDEELITSYLVNKISDSSFTGRAITDVDLNKCEPWDLPGKAKMGEKEWYFFSLRDRKYPTGVRTNRATNTGYWKTTGKDKEIFNSNTSDLVGMKKTLVFYRGRAPRGEKTNWVMHEYRVHAKSAFRTSKDEWVVCRVFQKSAGGKKYPSSSHSRSMINPYNLEIGPGSGYHQLPHQLMSNDPSYQFPVGLGRANNYMNNADFAEFSRVFRGNANMPLHDQSQINYPNGGGAECFTISGLN...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_025939`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_025939

Location Chr05:118757160-118759351 (-)

Description Similar to NAC098: Protein CUP-SHAPED COTYLEDON 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g53950`	Transcription activator of STM and KNAT6.	Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes.1999 · DOI: 10.1242/dev.126.8.1563 Involvement of CUP-SHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana.2000 · DOI: 10.1093/pcp/41.1.60 Roles of PIN-FORMED1 and MONOPTEROS in pattern formation of the apical region of the Arabidopsis embryo.2002 · DOI: 10.1242/dev.129.17.3965 The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli.2003 · DOI: 10.1093/pcp/pcg038 MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs.2004 · DOI: 10.1016/j.cub.2004.06.022 MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems.2004 · DOI: 10.1242/dev.01320 The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis.2005 · DOI: 10.1016/j.cub.2005.02.017 KNAT6: an Arabidopsis homeobox gene involved in meristem activity and organ separation.2006 · DOI: 10.1105/tpc.106.041988 The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis.2006 · DOI: 10.1105/tpc.106.045617 Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.2006 · DOI: 10.1105/tpc.106.045716 Plants expressing a miR164-resistant CUC2 gene reveal the importance of post-meristematic maintenance of phyllotaxy in Arabidopsis.2007 · DOI: 10.1242/dev.02774 Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness.2007 · DOI: 10.1242/dev.02817 Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant.1997 · DOI: 10.1105/tpc.9.6.841
`At5g61430`	Binds to the promoter regions of genes involved in chlorophyll catabolic processes, such as NYC1, SGR1, SGR2 and PAO.	No verified direct reference in this release
`At5g07680`	NAC domain-containing protein 79.	No verified direct reference in this release
`At5g39610`	Transcription activator that binds to DNA in promoters of target genes on a specific bipartite motif 5'-[ACG][CA]GT[AG](5-6n)[CT]AC[AG]-3'.	The delayed leaf senescence mutants of Arabidopsis, ore1, ore3, and ore9 are tolerant to oxidative stress.2004 · DOI: 10.1093/pcp/pch110 Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis.2009 · DOI: 10.1126/science.1166386 Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana.2009 · DOI: 10.1111/j.1364-3703.2009.00557.x A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence.2010 · DOI: 10.1111/j.1365-313x.2010.04151.x ORS1, an H₂O₂-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana.2011 · DOI: 10.1093/mp/ssq080 NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis.2013 · DOI: 10.1093/mp/sst012 ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription.2013 · DOI: 10.1038/embor.2013.24

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0460600`	Transcription factor involved in the regulation of tiller bud outgrowth, but does not seem to regulate tiller bud initiation.	Overexpression of a NAC-domain protein promotes shoot branching in rice.2007 · DOI: 10.1111/j.1469-8137.2007.02177.x OsNAC2 encoding a NAC transcription factor that affects plant height through mediating the gibberellic acid pathway in rice.2015 · DOI: 10.1111/tpj.12819 A Rice NAC Transcription Factor Promotes Leaf Senescence via ABA Biosynthesis.2017 · DOI: 10.1104/pp.17.00542 Overexpression of miR164b-resistant OsNAC2 improves plant architecture and grain yield in rice.2018 · DOI: 10.1093/jxb/ery017 OsNAC2 positively affects salt-induced cell death and binds to the OsAP37 and OsCOX11 promoters.2018 · DOI: 10.1111/tpj.13867 OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development.2020 · DOI: 10.1111/pbi.13209 Overexpression of a microRNA-targeted NAC transcription factor improves drought and salt tolerance in Rice via ABA-mediated pathways.2019 · DOI: 10.1186/s12284-019-0334-6 OsNAC2 Is Involved in Multiple Hormonal Pathways to Mediate Germination of Rice Seeds and Establishment of Seedling.2021 · DOI: 10.3389/fpls.2021.699303

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025939 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0010029 regulation of seed germination Biological Process

KEGG gene cross-reference

ath:AT5G07680

ath:AT5G39610

ath:AT5G53950

ath:AT5G61430

dosa:Os04g0460600

osa:4336052

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.959

Rank 1 · LXL04_025939 · OH-1004

Cytoplasm0.096

Rank 2 · LXL04_025939 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_025939 · OH-1004

Endoplasmic reticulum0.040

Rank 4 · LXL04_025939 · OH-1004

Plastid0.015

Rank 5 · LXL04_025939 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF02365.21NAM13-139 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025939	`PF02365.21`	NAM	13	139	1e-49	168.8

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O04017`	Arabidopsis thaliana	Protein CUP-SHAPED COTYLEDON 2	72.327%	Swiss-Prot	weak database homology
`Q9FLJ2`	Arabidopsis thaliana	NAC domain-containing protein 100	69.767%	Swiss-Prot	weak database homology
`Q9FLR3`	Arabidopsis thaliana	NAC domain-containing protein 79	67.039%	Swiss-Prot	moderate database homology
`Q9FKA0`	Arabidopsis thaliana	NAC domain-containing protein 92	65.363%	Swiss-Prot	moderate database homology
`Q7XUV6`	Oryza sativa subsp. japonica	NAC domain-containing protein 4	63.187%	Swiss-Prot	weak database homology

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