LXL04_001286 | RubberDandelionOmics

Gene overview

LXL04_001286

Reference: OH-1004 Chr: Chr01 Coordinates: 23434873-23438074 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2370 bp · LXL04_001286|LXL04_001286|OH1004|cDNA

ATGGCGTGTTCATCTTCCATCATAGGCGTATCCATATACCACAAAAACCCATCACTAGAGCAACTCTCCAGAAAAATTGCCGCCCCTGCCGCCCCCGTGCACCTTCCCCGTTCCACCGATAAAACTCACTTCACTTCCTTGAAAGTTACCTCCAAACTCAAACCTAACAGCACAGGTGTTTCTGGTGGTTCTGCTTTTGTTGCGTCGGCTACTGCCGCCCCCAATTCTGTTTTGAGTGAGAACGCGTTTAAGGGTTTTGG...

CDS

Download CDS FASTA

2370 bp · LXL04_001286|LXL04_001286|OH1004|CDS

ATGGCGTGTTCATCTTCCATCATAGGCGTATCCATATACCACAAAAACCCATCACTAGAGCAACTCTCCAGAAAAATTGCCGCCCCTGCCGCCCCCGTGCACCTTCCCCGTTCCACCGATAAAACTCACTTCACTTCCTTGAAAGTTACCTCCAAACTCAAACCTAACAGCACAGGTGTTTCTGGTGGTTCTGCTTTTGTTGCGTCGGCTACTGCCGCCCCCAATTCTGTTTTGAGTGAGAACGCGTTTAAGGGTTTTGG...

Protein

Download Protein FASTA

789 aa · LXL04_001286|LXL04_001286|OH1004|PROTEIN

MACSSSIIGVSIYHKNPSLEQLSRKIAAPAAPVHLPRSTDKTHFTSLKVTSKLKPNSTGVSGGSAFVASATAAPNSVLSENAFKGFGVFDEDSSLDDSDREYTDNSENEASIDIAAGNAGDDDELSITKLGLPQRLVQSLEKREITRLFPIQRAVLVPALEGRDIIARAKTGTGKTLAFGIPIIKRLTEDDEERISPRRGQKLPRVLVLAPTRELAKQVESEIKDSAPYLSTVCVYGGVSYNSQQNALSRGVDVVVGTPG...

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_001286`
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_001286

Location Chr01:23434873-23438074 (+)

Description Similar to RH3A: DEAD-box ATP-dependent RNA helicase 3A, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g26742`	Nuclear genome-encoded factor involved in ribosome biogenesis in chloroplasts.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0827700`	Nuclear genome-encoded factor involved in ribosome biogenesis in chloroplasts.	No verified direct reference in this release
`Os07g0143700`	DEAD-box ATP-dependent RNA helicase 53.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001286 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0042254 ribosome biogenesis Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0051607 defense response to virus Biological Process

GO:2000637 positive regulation of miRNA-mediated gene silencing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

KEGG gene cross-reference

ath:AT5G26742

dosa:Os03g0827700

dosa:Os07g0143700

zma:100191761

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.

Plastid0.962

Rank 1 · LXL04_001286 · OH-1004

Mitochondrion0.041

Rank 2 · LXL04_001286 · OH-1004

Nucleus0.029

Rank 3 · LXL04_001286 · OH-1004

Cytoplasm0.020

Rank 4 · LXL04_001286 · OH-1004

Peroxisome0.011

Rank 5 · LXL04_001286 · 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.

PF00270.36DEAD150-322 aa

PF04851.22ResIII163-316 aa

PF00271.38Helicase_C360-468 aa

PF26142.1DD_DDX21-DDX50504-552 aa

PF08152.19GUCT555-655 aa

PF00098.29zf-CCHC769-785 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001286	`PF00270.36`	DEAD	150	322	4.7e-47	160.5
LXL04_001286	`PF04851.22`	ResIII	163	316	8.9e-09	36.2
LXL04_001286	`PF00271.38`	Helicase_C	360	468	1.1e-33	116.5
LXL04_001286	`PF26142.1`	DD_DDX21-DDX50	504	552	4.5e-16	59.4
LXL04_001286	`PF08152.19`	GUCT	555	655	4e-16	59.7
LXL04_001286	`PF00098.29`	zf-CCHC	769	785	6e-07	30.0

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8L7S8`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 3, chloroplastic	71.151%	Swiss-Prot	strong database homology
`Q0DM51`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 3, chloroplastic	76.047%	Swiss-Prot	strong database homology
`Q0D8N0`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 53	61.461%	Swiss-Prot	moderate database homology

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