LXL04_018943 | RubberDandelionOmics

Gene overview

LXL04_018943

Reference: OH-1004 Chr: Chr04 Coordinates: 20276302-20282222 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4140 bp · LXL04_018943|LXL04_018943|OH1004|cDNA

TGTATCAGTGACTGGATTAAATCGTCATTTTAAAAGATTACATCCGATTAAAAGCATAACCAAAGAACcttgataaaaataatatattttggaactttaaattatttttgCACGAAGGATCCCAAGCCCCAATTCCATGGCCATCCTCTACGCAGGAAGAGGAGTCGTCAACGTTTGCCGACTTCCCGCCAAAGTTCGCCCACTTCCCTCTCCTTTCTCTCTGAGTCTCTGACTGTGATTTTCTTCCTACTCTAATTCCC...

CDS

Download CDS FASTA

3837 bp · LXL04_018943|LXL04_018943|OH1004|CDS

CTGTCCGGTGCTTACTCAACAATGGCATTTCGTCGCCCAACCAACGGTCGATCGCCGCTCGTTAATCCACAACGTCAAATAACCTCTTTCTTCTCCAAATCACCATCACCAACCTCCTCCCTTTCTCCCTCTCAATCACCATCCCCTCTTCTTTCTAACTCTAACTCTAAACTTAAACCTAAAACTAAACCTAGCCCTACAACCCCATCTCCCCTTCAACCCAAAAGCAGTAAAAAGCCGGCTTTAGTTATTGGTCAATC...

Protein

Download Protein FASTA

1278 aa · LXL04_018943|LXL04_018943|OH1004|PROTEIN

MSGAYSTMAFRRPTNGRSPLVNPQRQITSFFSKSPSPTSSLSPSQSPSPLLSNSNSKLKPKTKPSPTTPSPLQPKSSKKPALVIGQSSSTPASSAQNLIYGDELVNRRIKVYWPLDKAWYEGCVKSFDKSSGKHLVQYDDSEEEHLDLSKEKIELLKEQAKRFRRLRKFSIEDEDDDEAGGGSQEIVDKNVESGSDDSADEDWGKNVEKEAIDDEMEDLDLVDEEEEEEEVEMEETKAIKPEPKKRKSSAAAMKPASVKK...

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_018943`
TK1151 ID	TkA05G005050
OH-1004 ID	LXL04_018943
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.000
Protein coverage (%)	TK1151 94.762 / OH-1004 15.571 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_018943

Location Chr04:20276302-20282222 (-)

Description Similar to MSH6: DNA mismatch repair protein MSH6

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_018943 · 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.

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.

Nucleus0.943

Rank 1 · LXL04_018943 · OH-1004

Cytoplasm0.101

Rank 2 · LXL04_018943 · OH-1004

Cell membrane0.022

Rank 3 · LXL04_018943 · OH-1004

Plastid0.016

Rank 4 · LXL04_018943 · OH-1004

Mitochondrion0.016

Rank 5 · LXL04_018943 · 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_I347-460 aa

PF05188.24MutS_II471-554 aa

PF05192.24MutS_III659-974 aa

PF05190.24MutS_IV844-934 aa

PF00488.28MutS_V1036-1225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018943	`PF01624.26`	MutS_I	347	460	1.6e-31	109.5
LXL04_018943	`PF05188.24`	MutS_II	471	554	5.2e-09	37.4
LXL04_018943	`PF05192.24`	MutS_III	659	974	4.3e-35	122.5
LXL04_018943	`PF05190.24`	MutS_IV	844	934	4.5e-17	62.8
LXL04_018943	`PF00488.28`	MutS_V	1036	1225	1e-69	235.0

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
`O04716`	Arabidopsis thaliana	DNA mismatch repair protein MSH6	58.426%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card