LXL04_038945 | RubberDandelionOmics

Gene overview

LXL04_038945

Reference: OH-1004 Chr: Chr09 Coordinates: 54151244-54154067 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2373 bp · LXL04_038945|LXL04_038945|OH1004|cDNA

atgGGCTGCAAACAAAAGCCCTTTAATCACATGAACAAGAACAACATCTCCTGGCTTGGTGGACTGGTGGCCCCTGCTATACAGCTCTCTTGTCTGGCTCGGGGGTTTAAGCTTCTTCGCCATCATCGCCGATGGAGGTTTAACCTTTTATTTCCGACGAAAGAAATGGGTTTATCTCACATCATCCAACTCCGACGCCTGCTTCCTCGAAGCCCTTATCTCCATAAAACCATTTTCATCAGTCAACTGAATGTGAAGCC...

CDS

Download CDS FASTA

2373 bp · LXL04_038945|LXL04_038945|OH1004|CDS

ATGGGCTGCAAACAAAAGCCCTTTAATCACATGAACAAGAACAACATCTCCTGGCTTGGTGGACTGGTGGCCCCTGCTATACAGCTCTCTTGTCTGGCTCGGGGGTTTAAGCTTCTTCGCCATCATCGCCGATGGAGGTTTAACCTTTTATTTCCGACGAAAGAAATGGGTTTATCTCACATCATCCAACTCCGACGCCTGCTTCCTCGAAGCCCTTATCTCCATAAAACCATTTTCATCAGTCAACTGAATGTGAAGCC...

Protein

Download Protein FASTA

790 aa · LXL04_038945|LXL04_038945|OH1004|PROTEIN

MGCKQKPFNHMNKNNISWLGGLVAPAIQLSCLARGFKLLRHHRRWRFNLLFPTKEMGLSHIIQLRRLLPRSPYLHKTIFISQLNVKPFSSSTPASDQSNEKPTSLSARMSFVFDQIDAIEKERSEKDETLQRIRAWRESKKEKQPIIEHEETLKHTNDVTVSGFKEKGLMTKGVELVHPWPEWIELMERLVQQNYFDCRRKDEDKMISDSGFGDVGADGGFMAEVMEEGFDFTRDWKTVQTAGLNFGKDRFDILRSLPRQ...

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_038945`
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_038945

Location Chr09:54151244-54154067 (+)

Description Similar to VAR3: Zinc finger protein VAR3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g17790`	Probable component of some protein complex required for chloroplast and palisade cell development.	Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development.2004 · DOI: 10.1242/jcs.01360

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038945 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009658 chloroplast organization Biological Process

GO:1900871 chloroplast mRNA modification Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT5G17790

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.

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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.

Plastid0.453

Rank 1 · LXL04_038945 · OH-1004

Nucleus0.308

Rank 2 · LXL04_038945 · OH-1004

Mitochondrion0.184

Rank 3 · LXL04_038945 · OH-1004

Cytoplasm0.053

Rank 4 · LXL04_038945 · OH-1004

Cell membrane0.025

Rank 5 · LXL04_038945 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00641.24Zn_ribbon_RanBP404-432 aa

PF00641.24Zn_ribbon_RanBP438-465 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038945	`PF00641.24`	Zn_ribbon_RanBP	404	432	8.6e-13	48.0
LXL04_038945	`PF00641.24`	Zn_ribbon_RanBP	438	465	8.6e-13	48.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8S9K3`	Arabidopsis thaliana	Zinc finger protein VAR3, chloroplastic	32.056%	Swiss-Prot	weak database homology

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