LXL04_022524 | RubberDandelionOmics

Gene overview

LXL04_022524

Reference: OH-1004 Chr: Chr05 Coordinates: 118515-124374 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2721 bp · LXL04_022524|LXL04_022524|OH1004|cDNA

ATGGCGATTGGAAGAAGTAGGGCAAGTGAAAGAAGTAATTGCGAGAACTTGCGAGAACATGCCGCGTCGCACAAAGTTAAAAAGGCGTTCCGAAACCGGAAGGATGCCAAGAAGAGATCTCCTGGAAATGAAAACTATGATCCAAGAACTCTATATTTGCCTCCCAGCTTCCTGGAGAGTTTATCAGGTTGCCAGAGACAATGGTGGGAGTTCAAGTCACAAAATATGGATAAGATTCTATTTTTCAAGGTAAAAAGACC...

CDS

Download CDS FASTA

2721 bp · LXL04_022524|LXL04_022524|OH1004|CDS

ATGGCGATTGGAAGAAGTAGGGCAAGTGAAAGAAGTAATTGCGAGAACTTGCGAGAACATGCCGCGTCGCACAAAGTTAAAAAGGCGTTCCGAAACCGGAAGGATGCCAAGAAGAGATCTCCTGGAAATGAAAACTATGATCCAAGAACTCTATATTTGCCTCCCAGCTTCCTGGAGAGTTTATCAGGTTGCCAGAGACAATGGTGGGAGTTCAAGTCACAAAATATGGATAAGATTCTATTTTTCAAGGTAAAAAGACC...

Protein

Download Protein FASTA

906 aa · LXL04_022524|LXL04_022524|OH1004|PROTEIN

MAIGRSRASERSNCENLREHAASHKVKKAFRNRKDAKKRSPGNENYDPRTLYLPPSFLESLSGCQRQWWEFKSQNMDKILFFKVKRPVCIVFTILFCSSVYIFTELTTVSQGDQPHCGFPEKNFATNVEKLACKVVKREICGVVTKGTLLDGEMVAANPDASYLFAVSEASGNQDEHGDRIYGVCVVDVATSKIMIGQFEDDSECSGLSCLLSQLRPVEIIKPMKSLTPETEKVLVRQTKSPVINELIPLEEFWDAEKTT...

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_022524`
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_022524

Location Chr05:118515-124374 (-)

Description Similar to MSH6: DNA mismatch repair protein MSH6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02070`	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 Dissimilar mispair-recognition spectra of Arabidopsis DNA-mismatch-repair proteins MSH2MSH6 (MutSalpha) and MSH2MSH7 (MutSgamma).2003 · DOI: 10.1093/nar/gkg780 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_022524 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000710 meiotic mismatch repair Biological Process

GO:0006281 DNA repair Biological Process

GO:0006290 pyrimidine dimer repair Biological Process

GO:0006298 mismatch repair Biological Process

GO:0007095 mitotic G2 DNA damage checkpoint signaling Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0008340 determination of adult lifespan Biological Process

GO:0009411 response to UV Biological Process

GO:0032876 negative regulation of DNA endoreduplication Biological Process

GO:0045910 negative regulation of DNA recombination Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT4G02070

dme:Dmel_CG7003

hsa:2956

mmu:17688

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.

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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.

Nucleus0.631

Rank 1 · LXL04_022524 · OH-1004

Cytoplasm0.341

Rank 2 · LXL04_022524 · OH-1004

Mitochondrion0.070

Rank 3 · LXL04_022524 · OH-1004

Cell membrane0.037

Rank 4 · LXL04_022524 · OH-1004

Plastid0.032

Rank 5 · LXL04_022524 · 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_I64-131 aa

PF05188.24MutS_II163-248 aa

PF05192.24MutS_III371-616 aa

PF05190.24MutS_IV486-576 aa

PF00488.28MutS_V678-837 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022524	`PF01624.26`	MutS_I	64	131	1.4e-07	32.4
LXL04_022524	`PF05188.24`	MutS_II	163	248	2.5e-08	35.1
LXL04_022524	`PF05192.24`	MutS_III	371	616	9e-10	39.9
LXL04_022524	`PF05190.24`	MutS_IV	486	576	5.7e-17	62.5
LXL04_022524	`PF00488.28`	MutS_V	678	837	3.6e-57	194.1

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
`O04716`	Arabidopsis thaliana	DNA mismatch repair protein MSH6	58.863%	Swiss-Prot	strong database homology

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