LXL04_026715 | RubberDandelionOmics

Gene overview

LXL04_026715

Reference: OH-1004 Chr: Chr06 Coordinates: 1856649-1865659 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5790 bp · LXL04_026715|LXL04_026715|OH1004|cDNA

ATGCAATCCGGTGGCGGGGTCCAGCAGGGAGGAGGGGGTGGGCATGGGCGGAACATGGTTGCCGGACCACCATCTTCCTCCGCATCTCCGTCGTCATCTTCTTCGGCTGTTTCCACTCCTCAGTTGGGGTTTGATCCAATGCAGCAGCAGCAGCAACAGCAGAGACAGTCATTACAACAACAACTACTTCGAAACCCTGAAGGAAGAGAAGCAATGTTAGCCTATCAATCTGGAAACCTACAAGGAGTATTAGGAGGATC...

CDS

Download CDS FASTA

5790 bp · LXL04_026715|LXL04_026715|OH1004|CDS

ATGCAATCCGGTGGCGGGGTCCAGCAGGGAGGAGGGGGTGGGCATGGGCGGAACATGGTTGCCGGACCACCATCTTCCTCCGCATCTCCGTCGTCATCTTCTTCGGCTGTTTCCACTCCTCAGTTGGGGTTTGATCCAATGCAGCAGCAGCAGCAACAGCAGAGACAGTCATTACAACAACAACTACTTCGAAACCCTGAAGGAAGAGAAGCAATGTTAGCCTATCAATCTGGAAACCTACAAGGAGTATTAGGAGGATC...

Protein

Download Protein FASTA

1929 aa · LXL04_026715|LXL04_026715|OH1004|PROTEIN

MQSGGGVQQGGGGGHGRNMVAGPPSSSASPSSSSSAVSTPQLGFDPMQQQQQQQRQSLQQQLLRNPEGREAMLAYQSGNLQGVLGGSSSSNSIQIQQGQNRNNPNFDQQQHMMNNPYAQYAFQNQQKTRMSPIGPSKDQSKNPLDEVHLAVSSIPDQSQGQSQNQKQFAVPTSGGSMRPIMGGPQGGSMAAQLQAMQAMALERNIDLSLPQNAHFMAQLIPLMQAKMQKANESNNMGPTMPRQQQSMPPGHPGQSQGQGQ...

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_026715`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_026715

Location Chr06:1856649-1865659 (-)

Description Similar to BRM: ATP-dependent helicase BRM

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g46020`	ATPase subunit of a multiprotein complex equivalent of the SWI/SNF complex that acts by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.	No verified direct reference in this release
`At2g28290`	Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning.	No verified direct reference in this release
`At5g19310`	Probable chromatin-remodeling factor that is functionally redundant with CHR12 in root and shoot stem cell initiation and root apical meristem (RAM) and shoot apical meristem (SAM) maintenance.	Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects.2012 · DOI: 10.1111/tpj.12009 Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression.2014 · DOI: 10.1186/1471-2229-14-76 Reduced seed germination in Arabidopsis over-expressing SWI/SNF2 ATPase genes.2015 · DOI: 10.1111/ppl.12231
`At3g06010`	Probable chromatin-remodeling factor that is functionally redundant with CHR23 in root and shoot stem cell initiation, and root apical meristem (RAM) and shoot apical meristem (SAM) maintenance.	The SWI/SNF chromatin-remodeling gene AtCHR12 mediates temporary growth arrest in Arabidopsis thaliana upon perceiving environmental stress.2007 · DOI: 10.1111/j.1365-313x.2007.03185.x Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects.2012 · DOI: 10.1111/tpj.12009 Reduced seed germination in Arabidopsis over-expressing SWI/SNF2 ATPase genes.2015 · DOI: 10.1111/ppl.12231

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0144300`	Probable chromatin-remodeling factor involved in root and shoot stem cell initiation, and root apical meristem (RAM) and shoot apical meristem (SAM) maintenance.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026715 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0009408 response to heat Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009611 response to wounding Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010104 regulation of ethylene-activated signaling pathway Biological Process

GO:0010199 organ boundary specification between lateral organs and the meristem Biological Process

KEGG gene cross-reference

ath:AT2G28290

ath:AT2G46020

ath:AT3G06010

ath:AT5G19310

dosa:Os05g0144300

osa:4337784

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.

Nucleus0.952

Rank 1 · LXL04_026715 · OH-1004

Cytoplasm0.141

Rank 2 · LXL04_026715 · OH-1004

Cell membrane0.016

Rank 3 · LXL04_026715 · OH-1004

Mitochondrion0.015

Rank 4 · LXL04_026715 · OH-1004

Endoplasmic reticulum0.007

Rank 5 · LXL04_026715 · 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.

PF08880.17QLQ327-360 aa

PF04851.22ResIII832-992 aa

PF00176.30SNF2-rel_dom836-1139 aa

PF00270.36DEAD853-995 aa

PF00271.38Helicase_C1162-1273 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026715	`PF08880.17`	QLQ	327	360	1.7e-08	34.7
LXL04_026715	`PF04851.22`	ResIII	832	992	8e-11	42.8
LXL04_026715	`PF00176.30`	SNF2-rel_dom	836	1139	1.6e-85	287.4
LXL04_026715	`PF00270.36`	DEAD	853	995	2.3e-08	34.7
LXL04_026715	`PF00271.38`	Helicase_C	1162	1273	3.9e-24	85.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q6EVK6`	Arabidopsis thaliana	Chromatin remodeling ATPase BRAHMA	61.671%	Swiss-Prot	strong database homology
`F4IHS2`	Arabidopsis thaliana	Chromatin structure-remodeling complex protein SYD	40.256%	Swiss-Prot	weak database homology
`F4K128`	Arabidopsis thaliana	Probable ATP-dependent DNA helicase CHR23	40.156%	Swiss-Prot	weak database homology
`F4J9M5`	Arabidopsis thaliana	Probable ATP-dependent DNA helicase CHR12	39.244%	Swiss-Prot	weak database homology
`Q60EX7`	Oryza sativa subsp. japonica	Probable ATP-dependent DNA helicase CHR719	39.821%	Swiss-Prot	weak database homology

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