LXL04_013165 | RubberDandelionOmics

Gene overview

LXL04_013165

Reference: OH-1004 Chr: Chr03 Coordinates: 25265959-25269364 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2574 bp · LXL04_013165|LXL04_013165|OH1004|cDNA

ATGGCGGCCACTCTTATCATCAGGCCTTTAGCTTGCGTTTCCTCTCCTCCTCCTCATCCATCGCCCCCGCACCTTCCTTATGCTTCTTCTTTCAGATTATGGACGCCATTTCTCAGAGGAGGAAATGGAGTTTTCTCTTCTCCATTCAACAACCTCGACTTCCTTCACCGCCACAGTTCTTCCTCCTCCCAGTTTTCTTCCGTCATCGCTTTTAGTGCCATCGCTACTGGTCCTGATCGAATTGCTCGTTTTGAGAGCCA...

CDS

Download CDS FASTA

2574 bp · LXL04_013165|LXL04_013165|OH1004|CDS

ATGGCGGCCACTCTTATCATCAGGCCTTTAGCTTGCGTTTCCTCTCCTCCTCCTCATCCATCGCCCCCGCACCTTCCTTATGCTTCTTCTTTCAGATTATGGACGCCATTTCTCAGAGGAGGAAATGGAGTTTTCTCTTCTCCATTCAACAACCTCGACTTCCTTCACCGCCACAGTTCTTCCTCCTCCCAGTTTTCTTCCGTCATCGCTTTTAGTGCCATCGCTACTGGTCCTGATCGAATTGCTCGTTTTGAGAGCCA...

Protein

Download Protein FASTA

857 aa · LXL04_013165|LXL04_013165|OH1004|PROTEIN

MAATLIIRPLACVSSPPPHPSPPHLPYASSFRLWTPFLRGGNGVFSSPFNNLDFLHRHSSSSSQFSSVIAFSAIATGPDRIARFESHDSDTDPISIFNDKILKDQYSRRASGRSNTESDSGSGVSVSNEDVDKYIQMVKQQQQRGLRELKKGHMLRKGGSNNGDATFSYKVDPFTLEEGDYVVHKKVGIGRFISIRPSIPDGETTPIDYVYIQYADGVAKLPVKQASRFLYRYNLPNESSAPRGLGRLKDTSVWEKRKVK...

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_013165`
TK1151 ID	TkA02G513830
OH-1004 ID	LXL04_013165
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
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_013165

Location Chr03:25265959-25269364 (-)

Description Similar to At3g02060: ATP-dependent DNA helicase At3g02060, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02060`	Probable helicase.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013165 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000716 transcription-coupled nucleotide-excision repair, DNA damage recognition Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003678 DNA helicase activity Molecular Function

GO:0003684 damaged DNA binding Molecular Function

GO:0004386 helicase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0015616 DNA translocase activity Molecular Function

GO:0016787 hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT3G02060

sep:SE_2280

ser:SERP0141

sha:SH2508

syn:sll0377

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.

Plastid0.923

Rank 1 · LXL04_013165 · OH-1004

Mitochondrion0.097

Rank 2 · LXL04_013165 · OH-1004

Nucleus0.032

Rank 3 · LXL04_013165 · OH-1004

Cytoplasm0.032

Rank 4 · LXL04_013165 · OH-1004

Peroxisome0.018

Rank 5 · LXL04_013165 · 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.

PF02559.23CarD_TRCF_RID176-233 aa

PF04851.22ResIII303-463 aa

PF00270.36DEAD305-467 aa

PF00271.38Helicase_C507-611 aa

PF22590.3Cas3-like_C_2514-612 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013165	`PF02559.23`	CarD_TRCF_RID	176	233	2.8e-09	37.6
LXL04_013165	`PF04851.22`	ResIII	303	463	1.8e-09	38.5
LXL04_013165	`PF00270.36`	DEAD	305	467	3.8e-25	89.3
LXL04_013165	`PF00271.38`	Helicase_C	507	611	4.5e-24	85.5
LXL04_013165	`PF22590.3`	Cas3-like_C_2	514	612	5.5e-06	27.3

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
`F4JFJ3`	Arabidopsis thaliana	Probable ATP-dependent helicase At3g02060, chloroplastic	67.790%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card