LXL04_004068 | RubberDandelionOmics

Gene overview

LXL04_004068

Reference: OH-1004 Chr: Chr01 Coordinates: 124028272-124035331 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3963 bp · LXL04_004068|LXL04_004068|OH1004|cDNA

ATGAGTACGGTAGACAAGATGTTGATAAAAGGTATCCGGAGTTTCGATCCGGAGAACCGAAACGTCATCACCTTCTACAAGCCGTTAACGCTCATCGTTGGTCCTAACGGTGCTGGCAAAACTACTATTATCGAGTGCTTAAAGCTATCCTGTACGGGTGAATTGCCACCGAATGCTAGGTCTGGTCAGAGTTTCATCCATGATCCCaagGTTGCAGGGGAAACAGAAACAAAGGCCCAGATAAAGCTGCGGTTCAAGAC...

CDS

Download CDS FASTA

3963 bp · LXL04_004068|LXL04_004068|OH1004|CDS

ATGAGTACGGTAGACAAGATGTTGATAAAAGGTATCCGGAGTTTCGATCCGGAGAACCGAAACGTCATCACCTTCTACAAGCCGTTAACGCTCATCGTTGGTCCTAACGGTGCTGGCAAAACTACTATTATCGAGTGCTTAAAGCTATCCTGTACGGGTGAATTGCCACCGAATGCTAGGTCTGGTCAGAGTTTCATCCATGATCCCAAGGTTGCAGGGGAAACAGAAACAAAGGCCCAGATAAAGCTGCGGTTCAAGAC...

Protein

Download Protein FASTA

1320 aa · LXL04_004068|LXL04_004068|OH1004|PROTEIN

MSTVDKMLIKGIRSFDPENRNVITFYKPLTLIVGPNGAGKTTIIECLKLSCTGELPPNARSGQSFIHDPKVAGETETKAQIKLRFKTAAGKDVVCIRSFQLTQKASKMEYKAIESVLQTINPHTGEKVCLSYRCADMDREIPALMGVSKAILENVIFVHQDEANWPLQDSSTLKKKFDDIFSATRYTKALEVIKKLHKDQAQEIKLSQKDLEKLQILKDAAYKLRQSITQDHEESERLGSKMHDLELHLQDVDAKIRQTE...

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_004068`
TK1151 ID	TkA01G206660
OH-1004 ID	LXL04_004068
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.600
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

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_004068

Location Chr01:124028272-124035331 (+)

Description Similar to RAD50: DNA repair protein RAD50

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31970`	Component of the MRN complex, which plays a central role in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity and meiosis.	Disruption of the Arabidopsis RAD50 gene leads to plant sterility and MMS sensitivity.2001 · DOI: 10.1046/j.1365-313x.2001.00928.x RAD50 function is essential for telomere maintenance in Arabidopsis.2001 · DOI: 10.1073/pnas.98.4.1711 Homologous recombination in planta is stimulated in the absence of Rad50.2001 · DOI: 10.1093/embo-reports/kve069 Meiotic defects in the Arabidopsis rad50 mutant point to conservation of the MRX complex function in early stages of meiotic recombination.2004 · DOI: 10.1007/s00412-004-0309-1

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004068 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000019 regulation of mitotic recombination Biological Process

GO:0000722 telomere maintenance via recombination Biological Process

GO:0000723 telomere maintenance Biological Process

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

GO:0000729 DNA double-strand break processing Biological Process

GO:0006281 DNA repair Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006312 mitotic recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007004 telomere maintenance via telomerase Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

KEGG gene cross-reference

ath:AT2G31970

hsa:10111

rno:64012

xla:495064

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.

Nucleus0.884

Rank 1 · LXL04_004068 · OH-1004

Cytoplasm0.175

Rank 2 · LXL04_004068 · OH-1004

Mitochondrion0.025

Rank 3 · LXL04_004068 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_004068 · OH-1004

Golgi apparatus0.010

Rank 5 · LXL04_004068 · 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.

PF02463.26SMC_N4-96 aa

PF13476.13AAA_236-225 aa

PF13304.13AAA_2129-50 aa

PF13558.13SbcC_Walker_B1194-1263 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004068	`PF02463.26`	SMC_N	4	96	1.1e-06	29.0
LXL04_004068	`PF13476.13`	AAA_23	6	225	8e-37	128.6
LXL04_004068	`PF13304.13`	AAA_21	29	50	5.7e-12	46.9
LXL04_004068	`PF13558.13`	SbcC_Walker_B	1194	1263	3.5e-06	27.9

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
`Q9SL02`	Arabidopsis thaliana	DNA repair protein RAD50	62.121%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card