LXL04_021664 | RubberDandelionOmics

Gene overview

LXL04_021664

Reference: OH-1004 Chr: Chr04 Coordinates: 134544542-134551661 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3240 bp · LXL04_021664|LXL04_021664|OH1004|cDNA

ATGGGAAAGCAAAAACAACAAGCTATTTCCCGTTTCTTCGCTCCCAAACCAAAACCATCATCAACGTCGCCTCCACCGTCACCACCGCCGTCGCAATCACTTCTTCCGAACTCATCAACACCTCCCCCTAAAATCTCCGCCACCGTCACCTACTCCCCTCTCAAACGCCTCCGTACCTCCCAGCTCATATCTCCAATAAAAAAACCTCCCAAAAGCCCCCGATTATCCTCCAATCCCGACCTTGCGGAATCATCTCAACG...

CDS

Download CDS FASTA

3240 bp · LXL04_021664|LXL04_021664|OH1004|CDS

ATGGGAAAGCAAAAACAACAAGCTATTTCCCGTTTCTTCGCTCCCAAACCAAAACCATCATCAACGTCGCCTCCACCGTCACCACCGCCGTCGCAATCACTTCTTCCGAACTCATCAACACCTCCCCCTAAAATCTCCGCCACCGTCACCTACTCCCCTCTCAAACGCCTCCGTACCTCCCAGCTCATATCTCCAATAAAAAAACCTCCCAAAAGCCCCCGATTATCCTCCAATCCCGACCTTGCGGAATCATCTCAACG...

Protein

Download Protein FASTA

1079 aa · LXL04_021664|LXL04_021664|OH1004|PROTEIN

MGKQKQQAISRFFAPKPKPSSTSPPPSPPPSQSLLPNSSTPPPKISATVTYSPLKRLRTSQLISPIKKPPKSPRLSSNPDLAESSQRKPSPHSQNPKPPSSNPTLHEKFISKLLEPSDEDTSNVPSSDAKASLNPKYTPLEQQVVELKAKYKDVLLMIEVGYKFRFFGEDAENAAKVLGIYAHVDHNFLTASIPTFRLNVHVRRLVSAGYKVGVVKQTETASIKAHGSNKTGPFCRDLSALYTKATLEAAEDVGGGEEEC...

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_021664`
TK1151 ID	TkA05G415100
OH-1004 ID	LXL04_021664
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.000
Protein coverage (%)	TK1151 99.814 / OH-1004 99.815 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_021664

Location Chr04:134544542-134551661 (+)

Description Similar to MSH3: DNA mismatch repair protein MSH3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g25540`	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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021664 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006298 mismatch repair Biological Process

GO:0006312 mitotic recombination Biological Process

GO:0043570 maintenance of DNA repeat elements Biological Process

GO:0045910 negative regulation of DNA recombination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0016020 membrane Cellular Component

GO:0032302 MutSbeta complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003684 damaged DNA binding Molecular Function

GO:0003690 double-stranded DNA binding Molecular Function

KEGG gene cross-reference

act:ACLA_006180

ath:AT4G25540

hsa:4437

mmu:17686

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.

Nucleus0.934

Rank 1 · LXL04_021664 · OH-1004

Cytoplasm0.103

Rank 2 · LXL04_021664 · OH-1004

Plastid0.021

Rank 3 · LXL04_021664 · OH-1004

Cell membrane0.020

Rank 4 · LXL04_021664 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_021664 · 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.

PF01624.26MutS_I138-248 aa

PF05188.24MutS_II289-379 aa

PF05192.24MutS_III447-767 aa

PF00488.28MutS_V822-1024 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021664	`PF01624.26`	MutS_I	138	248	2.4e-24	86.5
LXL04_021664	`PF05188.24`	MutS_II	289	379	1.3e-06	29.6
LXL04_021664	`PF05192.24`	MutS_III	447	767	1.3e-36	127.5
LXL04_021664	`PF00488.28`	MutS_V	822	1024	1.3e-65	221.6

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
`O65607`	Arabidopsis thaliana	DNA mismatch repair protein MSH3	58.484%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card