LXL04_011386 | RubberDandelionOmics

Gene overview

LXL04_011386

Reference: OH-1004 Chr: Chr02 Coordinates: 163640850-163650265 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1497 bp · LXL04_011386|LXL04_011386|OH1004|cDNA

ATGCTTAAGAATCTCTGTCAAACCCTAAAATCATTACCCAGGAACCCCAGATCAACGATTTCGGTTTTTCATTTTCACACCCGCAAGAAAACCCTACTCTCCAATCCGGCGATAGATTTCATACTGAATGAAATCGCAGACCTCCCATCTTCAAACACCATTAAAACCCCAAtacaagatacaccaaaaaccGCAGAACAAGTTGACGCAGAAACATTGAGTATTGAGAATTTACACCCATGGCCGGAATGGGTTGTGTT...

CDS

Download CDS FASTA

1497 bp · LXL04_011386|LXL04_011386|OH1004|CDS

ATGCTTAAGAATCTCTGTCAAACCCTAAAATCATTACCCAGGAACCCCAGATCAACGATTTCGGTTTTTCATTTTCACACCCGCAAGAAAACCCTACTCTCCAATCCGGCGATAGATTTCATACTGAATGAAATCGCAGACCTCCCATCTTCAAACACCATTAAAACCCCAATACAAGATACACCAAAAACCGCAGAACAAGTTGACGCAGAAACATTGAGTATTGAGAATTTACACCCATGGCCGGAATGGGTTGTGTT...

Protein

Download Protein FASTA

498 aa · LXL04_011386|LXL04_011386|OH1004|PROTEIN

MLKNLCQTLKSLPRNPRSTISVFHFHTRKKTLLSNPAIDFILNEIADLPSSNTIKTPIQDTPKTAEQVDAETLSIENLHPWPEWVVLMQKLMKNGYLDVVSNPFRNGELIDGKACNQIRTACLNFARDRPDLMSYFTRGDIHAVAGSGCPSIDRKVVNSGKRLRAYIGIDEGNVCSSCDLRGKCERAYVKPREEEDGRTVDVMRFVLTYGLHHLNHSPDSEPYMNKRLEEAIRSLIGDMVKFSKTELDFDPSKCAPSVYR...

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_011386`
TK1151 ID	TkA03G585940
OH-1004 ID	LXL04_011386
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.400
Protein coverage (%)	TK1151 99.757 / OH-1004 88.353 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011386

Location Chr02:163640850-163650265 (-)

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_011386 · 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.

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.

Plastid0.347

Rank 1 · LXL04_011386 · OH-1004

Nucleus0.258

Rank 2 · LXL04_011386 · OH-1004

Cytoplasm0.190

Rank 3 · LXL04_011386 · OH-1004

Mitochondrion0.178

Rank 4 · LXL04_011386 · OH-1004

Cell membrane0.085

Rank 5 · LXL04_011386 · 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_RanBP286-310 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011386	`PF00641.24`	Zn_ribbon_RanBP	286	310	4.1e-10	39.5

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
`Q8S9K3`	Arabidopsis thaliana	Zinc finger protein VAR3, chloroplastic	31.660%	Swiss-Prot	moderate database homology

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