LXL04_028648 | RubberDandelionOmics

Gene overview

LXL04_028648

Reference: OH-1004 Chr: Chr06 Coordinates: 52073656-52081012 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3519 bp · LXL04_028648|LXL04_028648|OH1004|cDNA

ATGAGTACTCAAGTCTTGGAGAGGCAACAGAGCTCTTCATCGTTGCCAGAAGACCATATCGATAACACCAAGACTCTGATTTGTGCTCTTAGTTTCCTCTCTCGCAATCTCCCTCTCCCTCCTGACGTTTTCGATGCTGTCTCTTCCATCTACACCGCCGCCTCCGAAGATGTTGACGCCAACGTCCCCGAAGATGCCCACGCTGGTGTTGACGCTACCGCCCCCGGTGGATCTGACTGCGACAAACAAGTCGATGATGT...

CDS

Download CDS FASTA

3519 bp · LXL04_028648|LXL04_028648|OH1004|CDS

ATGAGTACTCAAGTCTTGGAGAGGCAACAGAGCTCTTCATCGTTGCCAGAAGACCATATCGATAACACCAAGACTCTGATTTGTGCTCTTAGTTTCCTCTCTCGCAATCTCCCTCTCCCTCCTGACGTTTTCGATGCTGTCTCTTCCATCTACACCGCCGCCTCCGAAGATGTTGACGCCAACGTCCCCGAAGATGCCCACGCTGGTGTTGACGCTACCGCCCCCGGTGGATCTGACTGCGACAAACAAGTCGATGATGT...

Protein

Download Protein FASTA

1172 aa · LXL04_028648|LXL04_028648|OH1004|PROTEIN

MSTQVLERQQSSSSLPEDHIDNTKTLICALSFLSRNLPLPPDVFDAVSSIYTAASEDVDANVPEDAHAGVDATAPGGSDCDKQVDDVSSPKNFQLQNGGDLMADLEEALLTHRSNHITGTEIAETRKKRIESHIQNRLTQLEELPTSRGEDLQSKCLLELYGLKLAELQRKVRSNVSSEYTLCLNCVYPEKQLFDWGMMRLSRPSYGVGDAFAVDSDNHLKKKRDAERLTKLEEEEKNRVETRKRKFFAEILNSIRELQL...

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_028648`
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_028648

Location Chr06:52073656-52081012 (+)

Description Similar to CHR12: Probable ATP-dependent DNA helicase CHR12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

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_028648 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006261 DNA-templated DNA replication Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0006338 chromatin remodeling Biological Process

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

GO:0007064 mitotic sister chromatid cohesion Biological Process

GO:0009408 response to heat Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010231 maintenance of seed dormancy Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

KEGG gene cross-reference

ath:AT3G06010

ath:AT5G19310

dosa:Os05g0144300

osa:4337784

sce:YOR290C

spo:2542638

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.

Nucleus0.853

Rank 1 · LXL04_028648 · OH-1004

Cytoplasm0.185

Rank 2 · LXL04_028648 · OH-1004

Mitochondrion0.037

Rank 3 · LXL04_028648 · OH-1004

Cell membrane0.027

Rank 4 · LXL04_028648 · OH-1004

Endoplasmic reticulum0.018

Rank 5 · LXL04_028648 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04851.22ResIII409-570 aa

PF00176.30SNF2-rel_dom413-700 aa

PF11496.15HDA2-3681-858 aa

PF00271.38Helicase_C719-832 aa

PF14619.12SnAC925-989 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028648	`PF04851.22`	ResIII	409	570	2.8e-11	44.3
LXL04_028648	`PF00176.30`	SNF2-rel_dom	413	700	1.9e-95	320.0
LXL04_028648	`PF11496.15`	HDA2-3	681	858	2.8e-10	40.5
LXL04_028648	`PF00271.38`	Helicase_C	719	832	8.6e-27	94.3
LXL04_028648	`PF14619.12`	SnAC	925	989	5.5e-10	40.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4J9M5`	Arabidopsis thaliana	Probable ATP-dependent DNA helicase CHR12	69.781%	Swiss-Prot	strong database homology
`F4K128`	Arabidopsis thaliana	Probable ATP-dependent DNA helicase CHR23	67.409%	Swiss-Prot	strong database homology
`Q60EX7`	Oryza sativa subsp. japonica	Probable ATP-dependent DNA helicase CHR719	63.163%	Swiss-Prot	strong database homology

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