Gene Annotation

Shows the current gene functional description, GO annotations, and KEGG cross-references. Functional annotations retain the source reference; direct Arabidopsis/rice sequence hits are shown separately.

Examples TkA01G624900 LXL04_000258 Reference examples LXL04_039733 TkAUNG001940

Search Results

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Gene ID	`LXL04_035480`
Query reference	OH1004
Location	Chr08:23339750-23343025 (+)
Description	Similar to NAC031: Protein CUP-SHAPED COTYLEDON 3 (Arabidopsis thaliana OX%3D3702)
Annotation source assembly	GCA_047496595.1_OSU_TarKok_2.0

Functional annotation source: OH1004 · LXL04_035480 · GCA_047496595.1_OSU_TarKok_2.0.

This query returns 15 GO annotations and 5 KEGG gene cross-references from the OH1004 annotation record. The download is scoped to this query; these records do not establish KEGG pathway membership.

Arabidopsis / Rice Reference Genes and Papers

Papers describe Arabidopsis or rice reference genes. Functional links to rubber dandelion are based on protein alignments from the queried assembly.

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76420`	Transcription activator.	The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis.2003 · DOI: 10.1105/tpc.012203 Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.2006 · DOI: 10.1105/tpc.106.045716
`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
`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
`At5g07680`	NAC domain-containing protein 79.	No verified direct reference in this release
`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

Rice

No hit for this species in the current source table.

GO / KEGG

These GO/KEGG records retain the OH1004 annotation source and original transfer evidence/coverage. Their source-species scope differs from the direct Arabidopsis/rice alignment table.

Type	ID	Name	Namespace	Evidence	Source
GO	GO:0006351	DNA-templated transcription	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=IEA:UniProtKB-KW	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0009908	flower development	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=IMP:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0010014	meristem initiation	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=IGI:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0010072	primary shoot apical meristem specification	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=TAS:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0010199	organ boundary specification between lateral organs and the meristem	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=IGI:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0010223	secondary shoot formation	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=IMP:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0048366	leaf development	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=5; identity=73.377; coverage=40.526; evalue=5.71e-74; UniProt GO evidence=IMP:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0048527	lateral root development	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=TAS:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0051782	negative regulation of cell division	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=IMP:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0090691	formation of plant organ boundary	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76; UniProt GO evidence=IGI:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0090709	regulation of timing of plant organ formation	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=5; identity=73.377; coverage=40.526; evalue=5.71e-74; UniProt GO evidence=IMP:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:1990641	response to iron ion starvation	Biological Process	Swiss-Prot reviewed homolog transfer; hit_rank=2; identity=61.026; coverage=51.316; evalue=1.01e-76; UniProt GO evidence=IDA:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0005634	nucleus	Cellular Component	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=ISM:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0000976	transcription cis-regulatory region binding	Molecular Function	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=IPI:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
GO	GO:0003700	DNA-binding transcription factor activity	Molecular Function	Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97; UniProt GO evidence=ISS:TAIR	UniProtKB/Swiss-Prot DAT 2026 current_release
KEGG	ath:AT1G76420	KEGG gene cross-reference from reviewed UniProt hit; pathway name pending		Swiss-Prot reviewed homolog transfer; hit_rank=1; identity=53.846; coverage=75.263; evalue=1.01e-97	UniProtKB/Swiss-Prot DAT 2026 current_release
KEGG	ath:AT3G15170	KEGG gene cross-reference from reviewed UniProt hit; pathway name pending		Swiss-Prot reviewed homolog transfer; hit_rank=3; identity=68.452; coverage=44.211; evalue=5.22e-76	UniProtKB/Swiss-Prot DAT 2026 current_release
KEGG	ath:AT5G07680	KEGG gene cross-reference from reviewed UniProt hit; pathway name pending		Swiss-Prot reviewed homolog transfer; hit_rank=4; identity=63.687; coverage=47.105; evalue=9.09e-75	UniProtKB/Swiss-Prot DAT 2026 current_release
KEGG	ath:AT5G53950	KEGG gene cross-reference from reviewed UniProt hit; pathway name pending		Swiss-Prot reviewed homolog transfer; hit_rank=5; identity=73.377; coverage=40.526; evalue=5.71e-74	UniProtKB/Swiss-Prot DAT 2026 current_release
KEGG	ath:AT5G61430	KEGG gene cross-reference from reviewed UniProt hit; pathway name pending		Swiss-Prot reviewed homolog transfer; hit_rank=2; identity=61.026; coverage=51.316; evalue=1.01e-76	UniProtKB/Swiss-Prot DAT 2026 current_release