LXL04_039027 | RubberDandelionOmics

Gene overview

LXL04_039027

Reference: OH-1004 Chr: Chr09 Coordinates: 57061281-57065563 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2322 bp · LXL04_039027|LXL04_039027|OH1004|cDNA

ATGGCGTGTTCTTCTTCCATCATAGGCGTCTCCTCCATTTTCCCGAAACCCCCTTCTCCACTAGAGCATCTCTCCAAGAAAACCACACCTTCACCTCCTTTAAGTTTTCCGTTTCCTTCCGATAAAACCCACCTCACTTCCCTATCCAGACTTAGACATAACAGCGCCGGCGTCGGCGGAGGTGGTTCTGCTTTCTTGGCGTCGGCAATTGCGGCGAGGAATTCCGTTCTGACTGAGGAGGCGTTTAAGGGTCTTGGTGT...

CDS

Download CDS FASTA

2322 bp · LXL04_039027|LXL04_039027|OH1004|CDS

ATGGCGTGTTCTTCTTCCATCATAGGCGTCTCCTCCATTTTCCCGAAACCCCCTTCTCCACTAGAGCATCTCTCCAAGAAAACCACACCTTCACCTCCTTTAAGTTTTCCGTTTCCTTCCGATAAAACCCACCTCACTTCCCTATCCAGACTTAGACATAACAGCGCCGGCGTCGGCGGAGGTGGTTCTGCTTTCTTGGCGTCGGCAATTGCGGCGAGGAATTCCGTTCTGACTGAGGAGGCGTTTAAGGGTCTTGGTGT...

Protein

Download Protein FASTA

773 aa · LXL04_039027|LXL04_039027|OH1004|PROTEIN

MACSSSIIGVSSIFPKPPSPLEHLSKKTTPSPPLSFPFPSDKTHLTSLSRLRHNSAGVGGGGSAFLASAIAARNSVLTEEAFKGLGVFDDDDAEYDDESEFEASVDGGNDGATADDDDELSVSRLGLPQRLVETLVKRGISKLFPIQRAVLVPALEGRDIIGRAKTGTGKTLAFAIPIIKRLTEEDEENRNRVAGRLPRVLVLAPTRELAKQVETEIQESAPYLRTVCVYGGVSYTLQKNQLSRGVDIVVGTPGRLIDLV...

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_039027`
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_039027

Location Chr09:57061281-57065563 (+)

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

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Functional annotation source: OH1004 · LXL04_039027 · 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.

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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.

Plastid0.932

Rank 1 · LXL04_039027 · OH-1004

Mitochondrion0.061

Rank 2 · LXL04_039027 · OH-1004

Nucleus0.044

Rank 3 · LXL04_039027 · OH-1004

Cytoplasm0.024

Rank 4 · LXL04_039027 · OH-1004

Cell membrane0.012

Rank 5 · LXL04_039027 · 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.

PF00270.36DEAD145-316 aa

PF04851.22ResIII164-310 aa

PF00271.38Helicase_C354-462 aa

PF26142.1DD_DDX21-DDX50498-547 aa

PF08152.19GUCT549-650 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039027	`PF00270.36`	DEAD	145	316	2.1e-46	158.5
LXL04_039027	`PF04851.22`	ResIII	164	310	4e-08	34.1
LXL04_039027	`PF00271.38`	Helicase_C	354	462	2.3e-33	115.5
LXL04_039027	`PF26142.1`	DD_DDX21-DDX50	498	547	3e-18	66.3
LXL04_039027	`PF08152.19`	GUCT	549	650	1.2e-14	54.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8L7S8`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 3, chloroplastic	68.741%	Swiss-Prot	strong database homology
`Q0DM51`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 3, chloroplastic	72.910%	Swiss-Prot	strong database homology
`Q0D8N0`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 53	60.759%	Swiss-Prot	moderate database homology

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