LXL04_002345 | RubberDandelionOmics

Gene overview

LXL04_002345

Reference: OH-1004 Chr: Chr01 Coordinates: 46715949-46718597 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1956 bp · LXL04_002345|LXL04_002345|OH1004|cDNA

CCGCCAATTCATTTTATCCTTTCTCAGTCAAGAACCCTAACTTTGTTCTCGCAAGTTTCCAGATCTCATTTCAACCGTTTCTTCACGATAAAACATTGCGCCCGACTTACTCAAATGCCTGTGAATTTGTCATCGAACGCTATCCCGGCGATTCTCGCTGGCGATACGAATTCGAAGCCGTTGCTACAGGTATTAGAAATCAAACTCCTCGGAACGTCACAGGAAAGGTACCGTTTAATTCTATCGGATTCCGTGTCGAC...

CDS

Download CDS FASTA

1914 bp · LXL04_002345|LXL04_002345|OH1004|CDS

TTGTTCTCGCAAGTTTCCAGATCTCATTTCAACCGTTTCTTCACGATAAAACATTGCGCCCGACTTACTCAAATGCCTGTGAATTTGTCATCGAACGCTATCCCGGCGATTCTCGCTGGCGATACGAATTCGAAGCCGTTGCTACAGGTATTAGAAATCAAACTCCTCGGAACGTCACAGGAAAGGTACCGTTTAATTCTATCGGATTCCGTGTCGACTCAGCAAACGATGCTCGCTACGCAGCTTAATGATCGAGTCAA...

Protein

Download Protein FASTA

637 aa · LXL04_002345|LXL04_002345|OH1004|PROTEIN

MFSQVSRSHFNRFFTIKHCARLTQMPVNLSSNAIPAILAGDTNSKPLLQVLEIKLLGTSQERYRLILSDSVSTQQTMLATQLNDRVKTGAVQNGSVVQLIEYICSTVQNRKIIVVLNMETIIPQCEIIGNPNMPTESDTISSHNPLSNGISSTRPNPTNTTNNNTQTYRPTVQPPYQPPPVYKPHGAITKNEAPPRIIPISVLNPYQGRWAIKARVTAKGDLRRYNNAKGDGKVFSFDLLDSDSGEIRVTCFNSVVDKFY...

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_002345`
TK1151 ID	TkA01G453330
OH-1004 ID	LXL04_002345
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 97.849 / 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

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_002345

Location Chr01:46715949-46718597 (+)

Description Similar to RPA1A: Replication protein A 70 kDa DNA-binding subunit A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g06510`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	Replication protein A (AtRPA1a) is required for class I crossover formation but is dispensable for meiotic DNA break repair.2009 · DOI: 10.1038/emboj.2008.295 Arabidopsis replication protein A 70a is required for DNA damage response and telomere length homeostasis.2009 · DOI: 10.1093/pcp/pcp140
`At4g19130`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release
`At5g45400`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0776800`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	Two types of replication protein A in seed plants.2005 · DOI: 10.1111/j.1742-4658.2005.04719.x Replication protein A (RPA1a) is required for meiotic and somatic DNA repair but is dispensable for DNA replication and homologous recombination in rice.2009 · DOI: 10.1104/pp.109.142877
`Os05g0111000`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002345 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0007004 telomere maintenance via telomerase Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0007140 male meiotic nuclear division Biological Process

GO:0007141 male meiosis I Biological Process

GO:0009555 pollen development Biological Process

GO:0048232 male gamete generation Biological Process

GO:0051026 chiasma assembly Biological Process

GO:0051321 meiotic cell cycle Biological Process

KEGG gene cross-reference

ath:AT2G06510

ath:AT4G19130

ath:AT5G45400

dosa:Os02g0776800

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.

Nucleus0.931

Rank 1 · LXL04_002345 · OH-1004

Cytoplasm0.229

Rank 2 · LXL04_002345 · OH-1004

Mitochondrion0.030

Rank 3 · LXL04_002345 · OH-1004

Cell membrane0.015

Rank 4 · LXL04_002345 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_002345 · 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.

PF04057.19Rep-A_N29-121 aa

PF01336.32tRNA_anti-codon212-292 aa

PF16900.12REPA_OB_2320-424 aa

PF08646.17Rep_fac-A_C479-630 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002345	`PF04057.19`	Rep-A_N	29	121	2e-30	105.5
LXL04_002345	`PF01336.32`	tRNA_anti-codon	212	292	1e-12	48.5
LXL04_002345	`PF16900.12`	REPA_OB_2	320	424	3.9e-29	101.2
LXL04_002345	`PF08646.17`	Rep_fac-A_C	479	630	2e-49	167.8

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
`Q9SKI4`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit A	64.780%	Swiss-Prot	strong database homology
`F4JSG3`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit E	47.392%	Swiss-Prot	moderate database homology
`Q9FHJ6`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit C	56.432%	Swiss-Prot	strong database homology
`Q6YZ49`	Oryza sativa subsp. japonica	Replication protein A 70 kDa DNA-binding subunit A	54.954%	Swiss-Prot	strong database homology
`Q65XV7`	Oryza sativa subsp. japonica	Replication protein A 70 kDa DNA-binding subunit C	49.582%	Swiss-Prot	moderate database homology

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