LXL04_001956 | RubberDandelionOmics

Gene overview

LXL04_001956

Reference: OH-1004 Chr: Chr01 Coordinates: 37958367-37959861 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1098 bp · LXL04_001956|LXL04_001956|OH1004|cDNA

ATGGAGTTTTTTACCCACCAGTTTGATAAAAACGCCGATTCTCAGTTACCACCTGGGTTCAGATTCCACCCTACGGATGAAGAACTCATCACCTGCTACCTTCTCCGGAAAGTTCTTGACGGAAGTTTCAACTGTCGTGCCATCGCCGAAGTTGATCTCAACAAATGCGAACCATGGGAGCTTCCTCTTTCTTTACAAATGGGTGATTTTTGTTTGTGGGTTGATCTTGATCAAACAGAGAGAGCGAAAATGGGGGAGAA...

CDS

Download CDS FASTA

1098 bp · LXL04_001956|LXL04_001956|OH1004|CDS

ATGGAGTTTTTTACCCACCAGTTTGATAAAAACGCCGATTCTCAGTTACCACCTGGGTTCAGATTCCACCCTACGGATGAAGAACTCATCACCTGCTACCTTCTCCGGAAAGTTCTTGACGGAAGTTTCAACTGTCGTGCCATCGCCGAAGTTGATCTCAACAAATGCGAACCATGGGAGCTTCCTCTTTCTTTACAAATGGGTGATTTTTGTTTGTGGGTTGATCTTGATCAAACAGAGAGAGCGAAAATGGGGGAGAA...

Protein

Download Protein FASTA

365 aa · LXL04_001956|LXL04_001956|OH1004|PROTEIN

MEFFTHQFDKNADSQLPPGFRFHPTDEELITCYLLRKVLDGSFNCRAIAEVDLNKCEPWELPLSLQMGDFCLWVDLDQTERAKMGEKEWYFFSLRDRKYPTGLRTNRATEAGYWKATGKDREIYSSKTSSFVGMKKTLVFYRGRAPKGEKSNWVMHEYRLEGKFAYHFLSKSSKDEWVISRVFQKSGTGAIGGGSCAAGGMKPAAVGMNCYSSTSASLPQLLDSSPYASATSAFTADHDGYSFDSNAASKEHVPCFSTAS...

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_001956`
TK1151 ID	TkA01G494430
OH-1004 ID	LXL04_001956
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	74.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_001956

Location Chr01:37958367-37959861 (+)

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
`At3g15170`	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 The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation.2001 · DOI: 10.1242/dev.128.7.1127 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 Developmental events and shoot apical meristem gene expression patterns during shoot development in Arabidopsis thaliana.2002 · DOI: 10.1046/j.1365-313x.2002.01479.x The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli.2003 · DOI: 10.1093/pcp/pcg038 Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis.2003 · DOI: 10.1046/j.1365-313x.2003.01759.x CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation.2003 · DOI: 10.1046/j.1365-313x.2003.01911.x 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 Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.2006 · DOI: 10.1105/tpc.106.045716 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
`At3g29035`	Transcription activator that binds to DNA in promoters of target genes on a specific bipartite motif 5'-[AG]CGT[AG](4- 5n)[AG][CT]ACGCAA-3'.	ORS1, an H₂O₂-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana.2011 · DOI: 10.1093/mp/ssq080

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001956 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009611 response to wounding Biological Process

GO:0009908 flower development Biological Process

GO:0010014 meristem initiation Biological Process

GO:0010072 primary shoot apical meristem specification Biological Process

GO:0010150 leaf senescence Biological Process

GO:0010223 secondary shoot formation Biological Process

GO:0042542 response to hydrogen peroxide Biological Process

GO:0048366 leaf development Biological Process

GO:0048527 lateral root development Biological Process

GO:0051782 negative regulation of cell division Biological Process

GO:0090691 formation of plant organ boundary Biological Process

KEGG gene cross-reference

ath:AT3G15170

ath:AT3G29035

ath:AT5G07680

ath:AT5G53950

ath:AT5G61430

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

Open Annotation Module

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.

Nucleus0.963

Rank 1 · LXL04_001956 · OH-1004

Cytoplasm0.090

Rank 2 · LXL04_001956 · OH-1004

Endoplasmic reticulum0.041

Rank 3 · LXL04_001956 · OH-1004

Cell membrane0.038

Rank 4 · LXL04_001956 · OH-1004

Plastid0.016

Rank 5 · LXL04_001956 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF02365.21NAM17-160 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001956	`PF02365.21`	NAM	17	160	5.9e-45	153.4

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	49.502%	Swiss-Prot	moderate database homology
`Q9FRV4`	Arabidopsis thaliana	Protein CUP-SHAPED COTYLEDON 1	55.078%	Swiss-Prot	strong database homology
`Q9FLJ2`	Arabidopsis thaliana	NAC domain-containing protein 100	50.163%	Swiss-Prot	strong database homology
`Q9FLR3`	Arabidopsis thaliana	NAC domain-containing protein 79	54.613%	Swiss-Prot	strong database homology
`Q9LJW3`	Arabidopsis thaliana	NAC domain-containing protein 59	42.091%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card