LXL04_038275 | RubberDandelionOmics

Gene overview

LXL04_038275

Reference: OH-1004 Chr: Chr09 Coordinates: 36224950-36228725 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2799 bp · LXL04_038275|LXL04_038275|OH1004|cDNA

ATGGAAGAAAAACACAATTccccggcgaccaccaccgaAACGGCACTATTATCGTCGGCTGAGCCACCATCTTCAAGGAGAAGAGGCGGAGGGCTGAAGAGGAAAGCGTCGAATATTAGCAACAGCAACGCATCGACTCCGCCTCCGTCTTCTTCGAAGCGTCAAACCCGAGAGAAACCCTCTCCAGTACTGTTTCCTCCGATCCACAATGGGCCGTGCACCAGAGCTCGCCTACAACCAAATTACGCCGATTCCACGTC...

CDS

Download CDS FASTA

2799 bp · LXL04_038275|LXL04_038275|OH1004|CDS

ATGGAAGAAAAACACAATTCCCCGGCGACCACCACCGAAACGGCACTATTATCGTCGGCTGAGCCACCATCTTCAAGGAGAAGAGGCGGAGGGCTGAAGAGGAAAGCGTCGAATATTAGCAACAGCAACGCATCGACTCCGCCTCCGTCTTCTTCGAAGCGTCAAACCCGAGAGAAACCCTCTCCAGTACTGTTTCCTCCGATCCACAATGGGCCGTGCACCAGAGCTCGCCTACAACCAAATTACGCCGATTCCACGTC...

Protein

Download Protein FASTA

932 aa · LXL04_038275|LXL04_038275|OH1004|PROTEIN

MEEKHNSPATTTETALLSSAEPPSSRRRGGGLKRKASNISNSNASTPPPSSSKRQTREKPSPVLFPPIHNGPCTRARLQPNYADSTSFWDSVTVNGEGEGSVLSTPGAAKVEEELLARKEAWEALESKIEADYDDLKSRDANAHVAPVSSGWFSWTKPHPLEEKALASFFNGKLENRTPEIYMEIRNSIMKKFHSNPTTQLEEKDLCDLSPSVGDLDAKKEVMEFLDYWGLINYHPFPEPDVIPSVADPDDTEISEKAEK...

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_038275`
TK1151 ID	TkA04G413110
OH-1004 ID	LXL04_038275
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.800
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_038275

Location Chr09:36224950-36228725 (+)

Description Similar to SWI3C: SWI/SNF complex subunit SWI3C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g21700`	Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes.	CHB2, a member of the SWI3 gene family, is a global regulator in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000004305.60407.8b SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development.2005 · DOI: 10.1105/tpc.105.031203
`At2g33610`	Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes.	AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time.2002 · DOI: 10.1093/nar/gkf458 CHB2, a member of the SWI3 gene family, is a global regulator in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000004305.60407.8b SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development.2005 · DOI: 10.1105/tpc.105.031203

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038275 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006303 double-strand break repair via nonhomologous end joining Biological Process

GO:0006337 nucleosome disassembly Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045815 transcription initiation-coupled chromatin remodeling Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G21700

ath:AT2G33610

sce:YFR037C

spo:2541851

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.

Nucleus0.960

Rank 1 · LXL04_038275 · OH-1004

Cytoplasm0.125

Rank 2 · LXL04_038275 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_038275 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_038275 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_038275 · 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.

PF04433.24SWIRM154-234 aa

PF00569.24ZZ316-351 aa

PF00249.38Myb_DNA-binding375-417 aa

PF13921.13Myb_DNA-bind_6377-417 aa

PF16495.11SWIRM-assoc_1763-798 aa

PF16495.11SWIRM-assoc_1816-864 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038275	`PF04433.24`	SWIRM	154	234	1.7e-19	70.6
LXL04_038275	`PF00569.24`	ZZ	316	351	2.5e-09	37.5
LXL04_038275	`PF00249.38`	Myb_DNA-binding	375	417	7.3e-11	42.7
LXL04_038275	`PF13921.13`	Myb_DNA-bind_6	377	417	1.6e-06	28.9
LXL04_038275	`PF16495.11`	SWIRM-assoc_1	763	798	4e-20	72.3
LXL04_038275	`PF16495.11`	SWIRM-assoc_1	816	864	4e-20	72.3

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
`Q9XI07`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3C	36.207%	Swiss-Prot	weak database homology
`Q84JG2`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3B	28.239%	Swiss-Prot	weak database homology

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