LXL04_009884 | RubberDandelionOmics

Gene overview

LXL04_009884

Reference: OH-1004 Chr: Chr02 Coordinates: 135339864-135344225 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2878 bp · LXL04_009884|LXL04_009884|OH1004|cDNA

atgagGGTAGTCGACAACATTGACAAAACAGTGGCGAGTCTAGATGGCTCTAAACAGAGAGTACATCACGTAAAAGGCGGTGCCATTGAATTGCATCAAACAAGAAAGAAGAAAGATCAAACTGACATTCCCTCTCAATTCTAATACCATCTTTTCTTCTCAATTCAAAGTTCCATCCCTAATGTCGTTAAACAGCTTCAAGGAAATCCTCAAACCCTGTACATACCAATCCCAATCACAAACTTCCTCCTCATACTCAC...

CDS

Download CDS FASTA

2793 bp · LXL04_009884|LXL04_009884|OH1004|CDS

TTGAATTGCATCAAACAAGAAAGAAGAAAGATCAAACTGACATTCCCTCTCAATTCTAATACCATCTTTTCTTCTCAATTCAAAGTTCCATCCCTAATGTCGTTAAACAGCTTCAAGGAAATCCTCAAACCCTGTACATACCAATCCCAATCACAAACTTCCTCCTCATACTCACAAACTTCGTCAACTCTAAACCCTAGAAAACCCCCCAAATCCTCTCTCGCTCAACAACTCTTACGACTCGAAGGTGATTATAGTTC...

Protein

Download Protein FASTA

930 aa · LXL04_009884|LXL04_009884|OH1004|PROTEIN

MNCIKQERRKIKLTFPLNSNTIFSSQFKVPSLMSLNSFKEILKPCTYQSQSQTSSSYSQTSSTLNPRKPPKSSLAQQLLRLEGDYSSFPTSLPTKQSKEFSQIKQQEPQLDDVIEVKIDDEEEEFKDLDKQNGFRIARPKLEAPQFFDPTGPYEPLVLSESGQDPVVQVPASINCRLLEHQREGVKFLYNLYKKNHGGILGDDMGLGKTIQAIAFLSAIYKKDEEHDTTTPPNKQTPKGPTLIICPSSVIQNWEIEFSKW...

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_009884`
TK1151 ID	TkA03G479960
OH-1004 ID	LXL04_009884
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 96.038 / OH-1004 99.032 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_009884

Location Chr02:135339864-135344225 (+)

Description Similar to SWI2: Switch 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g03750`	May be involved in early DNA damage response (By similarity).	Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination.2006 · DOI: 10.1534/genetics.105.051664
`At3g19210`	Dissociates RAD51 from nucleoprotein filaments formed on dsDNA.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009884 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0010332 response to gamma radiation Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0036297 interstrand cross-link repair Biological Process

GO:0045003 double-strand break repair via synthesis-dependent strand annealing Biological Process

GO:0051301 cell division Biological Process

GO:0051701 biological process involved in interaction with host Biological Process

GO:0071248 cellular response to metal ion Biological Process

GO:0071480 cellular response to gamma radiation Biological Process

GO:0097680 double-strand break repair via classical nonhomologous end joining Biological Process

KEGG gene cross-reference

ath:AT1G03750

ath:AT3G19210

hsa:375748

mmu:76251

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.

Nucleus0.883

Rank 1 · LXL04_009884 · OH-1004

Cytoplasm0.151

Rank 2 · LXL04_009884 · OH-1004

Mitochondrion0.035

Rank 3 · LXL04_009884 · OH-1004

Cell membrane0.024

Rank 4 · LXL04_009884 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_009884 · 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.

PF04851.22ResIII176-344 aa

PF00176.30SNF2-rel_dom180-451 aa

PF00270.36DEAD199-345 aa

PF00271.38Helicase_C569-681 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009884	`PF04851.22`	ResIII	176	344	1.4e-10	42.0
LXL04_009884	`PF00176.30`	SNF2-rel_dom	180	451	4.7e-67	226.8
LXL04_009884	`PF00270.36`	DEAD	199	345	7.5e-08	33.0
LXL04_009884	`PF00271.38`	Helicase_C	569	681	2e-25	89.9

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
`F4I2H2`	Arabidopsis thaliana	Switch 2	62.938%	Swiss-Prot	strong database homology
`Q0PCS3`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 25	32.770%	Swiss-Prot	moderate database homology

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