LXL04_030535 | RubberDandelionOmics

Gene overview

LXL04_030535

Reference: OH-1004 Chr: Chr06 Coordinates: 118204931-118209688 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2796 bp · LXL04_030535|LXL04_030535|OH1004|cDNA

ATGGATGGAGATTTGCAGGACCACAACAAACTTCCTGAGCTGAAATTAGATGCTAAACAAGCTCAAGGGTTTCTCACCTTCTTTAAGAAATTACCTAACGATGAAAAGGCCGTTCGCTTTTTCGATCGACGGGATTATTTCACAGCTCATGGCGAAAATGCTTCTTTCATCGCAAAAACATATTACCACACAACAACCGCCCTAAGACAAATCGGCAATGGATCTGATGCAGTATCCAGTGTATCTGTAAGTAAAAACAT...

CDS

Download CDS FASTA

2796 bp · LXL04_030535|LXL04_030535|OH1004|CDS

ATGGATGGAGATTTGCAGGACCACAACAAACTTCCTGAGCTGAAATTAGATGCTAAACAAGCTCAAGGGTTTCTCACCTTCTTTAAGAAATTACCTAACGATGAAAAGGCCGTTCGCTTTTTCGATCGACGGGATTATTTCACAGCTCATGGCGAAAATGCTTCTTTCATCGCAAAAACATATTACCACACAACAACCGCCCTAAGACAAATCGGCAATGGATCTGATGCAGTATCCAGTGTATCTGTAAGTAAAAACAT...

Protein

Download Protein FASTA

931 aa · LXL04_030535|LXL04_030535|OH1004|PROTEIN

MDGDLQDHNKLPELKLDAKQAQGFLTFFKKLPNDEKAVRFFDRRDYFTAHGENASFIAKTYYHTTTALRQIGNGSDAVSSVSVSKNMFETIVRDLLLERTDHSLELYEGSGSNWRLTKRGTPGNLGSFEDILFANNDMQDSPVIVAILPNFRENGCTIGLGYVDLSKRILGITEFLDDSHFTNVESCLVSLGCKECVLPSETSKSNECKPLYDVMSKCGVMVTERKKTEFKSRDLGQDLGRLVKGSNEPVRDLVSSFEFA...

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_030535`
TK1151 ID	TkA07G410060
OH-1004 ID	LXL04_030535
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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_030535

Location Chr06:118204931-118209688 (-)

Description Similar to MSH2: DNA mismatch repair protein MSH2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18524`	Component of the post-replicative DNA mismatch repair system (MMR).	Arabidopsis MutS homologs-AtMSH2, AtMSH3, AtMSH6, and a novel AtMSH7-form three distinct protein heterodimers with different specificities for mismatched DNA.2000 · DOI: 10.1105/tpc.12.6.991 Reduction of stability of arabidopsis genomic and transgenic DNA-repeat sequences (microsatellites) by inactivation of AtMSH2 mismatch-repair function.2003 · DOI: 10.1104/pp.103.023952 Dissimilar mispair-recognition spectra of Arabidopsis DNA-mismatch-repair proteins MSH2MSH6 (MutSalpha) and MSH2MSH7 (MutSgamma).2003 · DOI: 10.1093/nar/gkg780 The role of AtMSH2 in homologous recombination in Arabidopsis thaliana.2006 · DOI: 10.1038/sj.embor.7400577 The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis.2006 · DOI: 10.1111/j.1365-313x.2006.02657.x Impact of the loss of AtMSH2 on double-strand break-induced recombination between highly diverged homeologous sequences in Arabidopsis thaliana germinal tissues.2007 · DOI: 10.1007/s11103-006-9128-5 Regulation of plant MSH2 and MSH6 genes in the UV-B-induced DNA damage response.2011 · DOI: 10.1093/jxb/err001

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030535 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006119 oxidative phosphorylation Biological Process

GO:0006281 DNA repair Biological Process

GO:0006290 pyrimidine dimer repair Biological Process

GO:0006298 mismatch repair Biological Process

GO:0006301 DNA damage tolerance Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0006312 mitotic recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007281 germ cell development Biological Process

GO:0008340 determination of adult lifespan Biological Process

GO:0010165 response to X-ray Biological Process

GO:0010224 response to UV-B Biological Process

KEGG gene cross-reference

ath:AT3G18524

bta:533115

mmu:17685

zma:100279876

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.

Nucleus0.774

Rank 1 · LXL04_030535 · OH-1004

Cytoplasm0.297

Rank 2 · LXL04_030535 · OH-1004

Mitochondrion0.058

Rank 3 · LXL04_030535 · OH-1004

Cell membrane0.033

Rank 4 · LXL04_030535 · OH-1004

Endoplasmic reticulum0.020

Rank 5 · LXL04_030535 · 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.

PF01624.26MutS_I23-128 aa

PF05188.24MutS_II143-283 aa

PF05192.24MutS_III299-606 aa

PF05190.24MutS_IV468-565 aa

PF00488.28MutS_V662-852 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030535	`PF01624.26`	MutS_I	23	128	8.6e-17	62.1
LXL04_030535	`PF05188.24`	MutS_II	143	283	7.8e-16	59.4
LXL04_030535	`PF05192.24`	MutS_III	299	606	7.4e-34	118.5
LXL04_030535	`PF05190.24`	MutS_IV	468	565	3.6e-20	72.8
LXL04_030535	`PF00488.28`	MutS_V	662	852	6.9e-81	271.4

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
`O24617`	Arabidopsis thaliana	DNA mismatch repair protein MSH2	73.746%	Swiss-Prot	strong database homology

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