LXL04_029908 | RubberDandelionOmics

Gene overview

LXL04_029908

Reference: OH-1004 Chr: Chr06 Coordinates: 103186034-103189755 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2403 bp · LXL04_029908|LXL04_029908|OH1004|cDNA

TGTTTTGGGGAAGATTCATTGCAAACCCTTCTCCCCCTTCTCTCTCTATCGTGTTTTTCTTGTCCTCTCTCTCCACAGACTTCCACCATTCACGGACCCCACAATTCCTCTAAACCCCTTCTTCTCCCCCTTCCTTCTCTCTtctcctttctctctctcgCTGCAATAATGCCAGCCTCCTCCTCAGAGACAAGGAACAGGTGGAGGAAACGGAAGCGAGGAGAGCAGTCCCGAAAACCTAGACCCCACGACGAAGACGA...

CDS

Download CDS FASTA

2385 bp · LXL04_029908|LXL04_029908|OH1004|CDS

TTGCAAACCCTTCTCCCCCTTCTCTCTCTATCGTGTTTTTCTTGTCCTCTCTCTCCACAGACTTCCACCATTCACGGACCCCACAATTCCTCTAAACCCCTTCTTCTCCCCCTTCCTTCTCTCTTCTCCTTTCTCTCTCTCGCTGCAATAATGCCAGCCTCCTCCTCAGAGACAAGGAACAGGTGGAGGAAACGGAAGCGAGGAGAGCAGTCCCGAAAACCTAGACCCCACGACGAAGACGATGAGGATTATGAAGAAGA...

Protein

Download Protein FASTA

794 aa · LXL04_029908|LXL04_029908|OH1004|PROTEIN

MQTLLPLLSLSCFSCPLSPQTSTIHGPHNSSKPLLLPLPSLFSFLSLAAIMPASSSETRNRWRKRKRGEQSRKPRPHDEDDEDYEEEDDVDLDQQNSHPEFDDGPSNSPDPTAATGAETEVISDGAVRISTFPSVIKHTVNQHHYSVIQSVARERACRTGDSSNGGLNYVFLENISHGQLQALSAMPKDAPALTGGDSEGSFVITPPPIMEGRGVVKRYGLDRVHVVPMHADWFSPTTVNRLERQAVPHFFSGKSPDHTP...

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_029908`
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_029908

Location Chr06:103186034-103189755 (+)

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
`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
`At4g34430`	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

Rice

Reference gene ID	Possible function	Papers / DOI
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_029908 · 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:2000070 regulation of response to water deprivation Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G21700

ath:AT2G47620

ath:AT4G34430

dosa:Os11g0183700

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.

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.

Nucleus0.944

Rank 1 · LXL04_029908 · OH-1004

Cytoplasm0.101

Rank 2 · LXL04_029908 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_029908 · OH-1004

Plastid0.017

Rank 4 · LXL04_029908 · OH-1004

Endoplasmic reticulum0.016

Rank 5 · LXL04_029908 · 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.

PF04433.24SWIRM235-314 aa

PF00249.38Myb_DNA-binding451-491 aa

PF13921.13Myb_DNA-bind_6452-493 aa

PF16495.11SWIRM-assoc_1631-705 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029908	`PF04433.24`	SWIRM	235	314	2.7e-21	76.3
LXL04_029908	`PF00249.38`	Myb_DNA-binding	451	491	9.9e-10	39.1
LXL04_029908	`PF13921.13`	Myb_DNA-bind_6	452	493	1e-06	29.5
LXL04_029908	`PF16495.11`	SWIRM-assoc_1	631	705	3e-25	88.7

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	51.359%	Swiss-Prot	strong database homology
`Q8W475`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3A	29.688%	Swiss-Prot	weak database homology
`Q8VY05`	Arabidopsis thaliana	SWI/SNF complex subunit SWI3D	35.216%	Swiss-Prot	weak database homology
`Q53KK6`	Oryza sativa subsp. japonica	SWI/SNF complex subunit SWI3C homolog	43.613%	Swiss-Prot	moderate database homology

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