LXL04_025889 | RubberDandelionOmics

Gene overview

LXL04_025889

Reference: OH-1004 Chr: Chr05 Coordinates: 118198050-118201096 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2598 bp · LXL04_025889|LXL04_025889|OH1004|cDNA

ATGGCGGTTCAACTGACGGAAGGCGCAATAGCAATGATATGTACTGGACAATGGGAACCGGCGGACGTGCAACCTGTGCTTCAGGTGACGGATCTTCGGATTGTTTCGACACAGAATTCTTCTTCTGGAAAAGTGGATAGATACCGGCTTATGCTATCTGATGGTACGTTTTCTCAGCAAGGGATGCTTGCTACTCAGCAGAATGATTTGGTTAGATGTAACCAGATGCAGAAGGGCTCTATTGTTCGGTTGAAGGACTA...

CDS

Download CDS FASTA

2598 bp · LXL04_025889|LXL04_025889|OH1004|CDS

ATGGCGGTTCAACTGACGGAAGGCGCAATAGCAATGATATGTACTGGACAATGGGAACCGGCGGACGTGCAACCTGTGCTTCAGGTGACGGATCTTCGGATTGTTTCGACACAGAATTCTTCTTCTGGAAAAGTGGATAGATACCGGCTTATGCTATCTGATGGTACGTTTTCTCAGCAAGGGATGCTTGCTACTCAGCAGAATGATTTGGTTAGATGTAACCAGATGCAGAAGGGCTCTATTGTTCGGTTGAAGGACTA...

Protein

Download Protein FASTA

865 aa · LXL04_025889|LXL04_025889|OH1004|PROTEIN

MAVQLTEGAIAMICTGQWEPADVQPVLQVTDLRIVSTQNSSSGKVDRYRLMLSDGTFSQQGMLATQQNDLVRCNQMQKGSIVRLKDYLRNMIQERMYFVSKLDFLMCGGFNVETVTNLIYSLVVLDQCYCNIHTSLSITFINHCLKFVWHPFISFFSILIIINIEVIVPFCEPIGQPKAFPVRSSSEPPSPIQAFNQPAITSTTPQTFMGHNSFPRPANSPIYPPNQEHNTAFHSYGNNPMSPHSIPSFSRSPTTTTTYI...

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_025889`
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_025889

Location Chr05:118198050-118201096 (-)

Description Similar to RPA1C: Replication protein A 70 kDa DNA-binding subunit C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g45400`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release
`At4g19130`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0111000`	Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication.	No verified direct reference in this release
`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

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025889 · 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:0006289 nucleotide-excision repair Biological Process

GO:0007004 telomere maintenance via telomerase Biological Process

GO:0007140 male meiotic nuclear division Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005662 DNA replication factor A complex Cellular Component

GO:0003684 damaged DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0043047 single-stranded telomeric DNA binding Molecular Function

KEGG gene cross-reference

ath:AT4G19130

ath:AT5G45400

dosa:Os05g0111000

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.

Nucleus0.901

Rank 1 · LXL04_025889 · OH-1004

Cytoplasm0.230

Rank 2 · LXL04_025889 · OH-1004

Mitochondrion0.027

Rank 3 · LXL04_025889 · OH-1004

Cell membrane0.022

Rank 4 · LXL04_025889 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_025889 · 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_N5-104 aa

PF01336.32tRNA_anti-codon304-374 aa

PF16900.12REPA_OB_2414-517 aa

PF08646.17Rep_fac-A_C571-718 aa

PF00098.29zf-CCHC823-838 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025889	`PF04057.19`	Rep-A_N	5	104	2.2e-22	79.7
LXL04_025889	`PF01336.32`	tRNA_anti-codon	304	374	2.2e-12	47.4
LXL04_025889	`PF16900.12`	REPA_OB_2	414	517	2.1e-31	108.5
LXL04_025889	`PF08646.17`	Rep_fac-A_C	571	718	4.4e-49	166.7
LXL04_025889	`PF00098.29`	zf-CCHC	823	838	1e-07	32.4

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
`Q9FHJ6`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit C	43.370%	Swiss-Prot	moderate database homology
`F4JSG3`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit E	49.213%	Swiss-Prot	moderate database homology
`Q9SKI4`	Arabidopsis thaliana	Replication protein A 70 kDa DNA-binding subunit A	44.953%	Swiss-Prot	moderate database homology
`Q65XV7`	Oryza sativa subsp. japonica	Replication protein A 70 kDa DNA-binding subunit C	39.203%	Swiss-Prot	moderate database homology
`Q6YZ49`	Oryza sativa subsp. japonica	Replication protein A 70 kDa DNA-binding subunit A	44.490%	Swiss-Prot	moderate database homology

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