LXL04_009353 | RubberDandelionOmics

Gene overview

LXL04_009353

Reference: OH-1004 Chr: Chr02 Coordinates: 123881531-123883981 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1830 bp · LXL04_009353|LXL04_009353|OH1004|cDNA

ATGGAGAGCTCACACCACCAGTTTTTAAAACCATTCCTTCCCGCCGACGATCACCGCTTCGAATTCGAACTCTACACCATCCCCAGCAGCTCCGGTTGGTTTTCTTGGGATAGCATTCACGAAACCGAGAAAAGCTCACTCAAGGAGTTTTTCGACGGGAGTTCGCTTACCAGAAACCCTAGGGTGTATAAAGAGTATCGTGATTTCATTATTTCAAAGTACAGGGAAGATCCTTTTAGAAGGCTAACCTTCTCCGAAGT...

CDS

Download CDS FASTA

1830 bp · LXL04_009353|LXL04_009353|OH1004|CDS

ATGGAGAGCTCACACCACCAGTTTTTAAAACCATTCCTTCCCGCCGACGATCACCGCTTCGAATTCGAACTCTACACCATCCCCAGCAGCTCCGGTTGGTTTTCTTGGGATAGCATTCACGAAACCGAGAAAAGCTCACTCAAGGAGTTTTTCGACGGGAGTTCGCTTACCAGAAACCCTAGGGTGTATAAAGAGTATCGTGATTTCATTATTTCAAAGTACAGGGAAGATCCTTTTAGAAGGCTAACCTTCTCCGAAGT...

Protein

Download Protein FASTA

609 aa · LXL04_009353|LXL04_009353|OH1004|PROTEIN

MESSHHQFLKPFLPADDHRFEFELYTIPSSSGWFSWDSIHETEKSSLKEFFDGSSLTRNPRVYKEYRDFIISKYREDPFRRLTFSEVRKSLVGDVNYLLKVFLFLEKWGLINFGAQSPSSASGGEDDDVVTENVEEERWKVKVEEGPPHGVRVVAIPNSLKPVALPTTASSINGSHLADSDFKMPPLSSHSDVYQELIDSVCGNCKELCESGHYEYTKDKTSIICIKCFENGAYGKNKSIDDYKLIDSTPDNKNKVTPWT...

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_009353`
TK1151 ID	TkA03G428500
OH-1004 ID	LXL04_009353
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.400
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_009353

Location Chr02:123881531-123883981 (+)

Description Similar to SWI3A: SWI/SNF complex subunit SWI3A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g47620`	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.	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

Reference gene ID	Possible function	Papers / DOI
`Os04g0480300`	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.	No verified direct reference in this release
`Os11g0183700`	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.	A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice.2020 · DOI: 10.1111/nph.16518

Functional annotation source

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Functional annotation source: OH1004 · LXL04_009353 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription 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

GO:0005737 cytoplasm Cellular Component

GO:0016514 SWI/SNF complex Cellular Component

GO:0016586 RSC-type complex Cellular Component

KEGG gene cross-reference

ath:AT2G33610

ath:AT2G47620

dosa:Os04g0480300

spo:2541851

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.

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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.

Nucleus0.957

Rank 1 · LXL04_009353 · OH-1004

Cytoplasm0.107

Rank 2 · LXL04_009353 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_009353 · OH-1004

Mitochondrion0.013

Rank 4 · LXL04_009353 · OH-1004

Plastid0.010

Rank 5 · LXL04_009353 · 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.

PF04433.24SWIRM35-113 aa

PF00249.38Myb_DNA-binding258-299 aa

PF16495.11SWIRM-assoc_1513-586 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009353	`PF04433.24`	SWIRM	35	113	2e-23	83.1
LXL04_009353	`PF00249.38`	Myb_DNA-binding	258	299	1.6e-08	35.3
LXL04_009353	`PF16495.11`	SWIRM-assoc_1	513	586	1.1e-15	58.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8W475`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3A	48.916%	Swiss-Prot	moderate database homology
`Q84JG2`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3B	29.260%	Swiss-Prot	weak database homology
`Q0JCC3`	Oryza sativa subsp. japonica	SWI/SNF complex subunit SWI3A homolog	35.372%	Swiss-Prot	moderate database homology
`Q53KK6`	Oryza sativa subsp. japonica	SWI/SNF complex subunit SWI3C homolog	30.796%	Swiss-Prot	weak database homology

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