LXL04_001138 | RubberDandelionOmics

Gene overview

LXL04_001138

Reference: OH-1004 Chr: Chr01 Coordinates: 20969333-20972966 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2700 bp · LXL04_001138|LXL04_001138|OH1004|cDNA

ATGAAAGACGATTGAGTAGATTTATCGACCATGACATCTCCATCGATTAAACCTATAAACAAGAGTGCCATCCACAAAATCTGCGCAGGCCAAGTGATTTTGGACCTCCCCTCCGCCGTTAAGGAATTGGTCGAGAACAGTTTGGATGCCGGCTCCATCAGCATTGAGGTTGCCCTAAAGGAATACGGCGAAGAATCGTTTCAAGTCATTGATAATGGCTGTGGCATTTCGCCAGACAATTTCAAGGTTCTAGCGCTTAA...

CDS

Download CDS FASTA

2670 bp · LXL04_001138|LXL04_001138|OH1004|CDS

ATGACATCTCCATCGATTAAACCTATAAACAAGAGTGCCATCCACAAAATCTGCGCAGGCCAAGTGATTTTGGACCTCCCCTCCGCCGTTAAGGAATTGGTCGAGAACAGTTTGGATGCCGGCTCCATCAGCATTGAGGTTGCCCTAAAGGAATACGGCGAAGAATCGTTTCAAGTCATTGATAATGGCTGTGGCATTTCGCCAGACAATTTCAAGGTTCTAGCGCTTAAGCATCATACGTCGAAATTAGCGGATTTTTC...

Protein

Download Protein FASTA

889 aa · LXL04_001138|LXL04_001138|OH1004|PROTEIN

MTSPSIKPINKSAIHKICAGQVILDLPSAVKELVENSLDAGSISIEVALKEYGEESFQVIDNGCGISPDNFKVLALKHHTSKLADFSDLQSVTTFGFRGEALSALCYLGDLTVETRTKSEQVATHLTFGRSGLLTEEKKTARQVGTTVTVKKLFSNLPVRSKEFHRNIRKEYGKLISLLNAYALTAKGVRLVCTNTTVNNKTSVVLKTQGSGSFKDNIITVFGMNTFNCLEPLSLVISDSCKVDGFLSKSGNGSGRNIGD...

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_001138`
TK1151 ID	TkA01G558130
OH-1004 ID	LXL04_001138
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
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_001138

Location Chr01:20969333-20972966 (+)

Description Similar to PMS1: DNA mismatch repair protein PMS1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02460`	Required for DNA mismatch repair (MMR), correcting base-base mismatches and insertion-deletion loops (IDLs) resulting from DNA replication, DNA damage or from recombination events between non- identical sequences during meiosis.	Involvement of the Arabidopsis thaliana AtPMS1 gene in somatic repeat instability.2004 · DOI: 10.1007/s11103-004-3472-0 The Arabidopsis DNA mismatch repair gene PMS1 restricts somatic recombination between homeologous sequences.2009 · DOI: 10.1007/s11103-008-9447-9 Yeast mutator phenotype enforced by Arabidopsis PMS1 expression.2013 · DOI: 10.1007/s11033-012-2269-5

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_001138 · 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:0006298 mismatch repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007095 mitotic G2 DNA damage checkpoint signaling Biological Process

GO:0009555 pollen development Biological Process

GO:0010154 fruit development Biological Process

GO:0048316 seed development Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT4G02460

gga:101752182

hsa:5395

mmu:18861

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.

Nucleus0.908

Rank 1 · LXL04_001138 · OH-1004

Cytoplasm0.192

Rank 2 · LXL04_001138 · OH-1004

Mitochondrion0.036

Rank 3 · LXL04_001138 · OH-1004

Cell membrane0.021

Rank 4 · LXL04_001138 · OH-1004

Golgi apparatus0.012

Rank 5 · LXL04_001138 · 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.

PF02518.32HATPase_c25-94 aa

PF13589.13HATPase_c_328-127 aa

PF01119.26DNA_mis_repair218-337 aa

PF08676.17MutL_C685-841 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001138	`PF02518.32`	HATPase_c	25	94	3.2e-06	28.2
LXL04_001138	`PF13589.13`	HATPase_c_3	28	127	5.8e-14	53.0
LXL04_001138	`PF01119.26`	DNA_mis_repair	218	337	2.1e-24	86.2
LXL04_001138	`PF08676.17`	MutL_C	685	841	7.6e-25	88.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q941I6`	Arabidopsis thaliana	DNA mismatch repair protein PMS1	55.677%	Swiss-Prot	strong database homology

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