LXL04_022280 | RubberDandelionOmics

Gene overview

LXL04_022280

Reference: OH-1004 Chr: Chr04 Coordinates: 147500200-147502144 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1290 bp · LXL04_022280|LXL04_022280|OH1004|cDNA

ATGGCAGCAGCTGCCACTAGATTCTTCTCTCTGTTCGAAAGCAACgccacctccaccgccaccaCAGCCGCAAACCTGTACCCGTTCCGTGCAATTCGATTACAACCGACACTCTTCTGTTCTCCAACCCTACGATTCCGTCGCTACTCGTCTTCCTCCGCTGCCGTGATAGAAAATGATTCTCCCACCACCGCCACCCTTGGTGAAACAACGGAAGCCTCCCACCAACATCCATGGCCGGAGTGGGTGACTTTCGTTGA...

CDS

Download CDS FASTA

1290 bp · LXL04_022280|LXL04_022280|OH1004|CDS

ATGGCAGCAGCTGCCACTAGATTCTTCTCTCTGTTCGAAAGCAACGCCACCTCCACCGCCACCACAGCCGCAAACCTGTACCCGTTCCGTGCAATTCGATTACAACCGACACTCTTCTGTTCTCCAACCCTACGATTCCGTCGCTACTCGTCTTCCTCCGCTGCCGTGATAGAAAATGATTCTCCCACCACCGCCACCCTTGGTGAAACAACGGAAGCCTCCCACCAACATCCATGGCCGGAGTGGGTGACTTTCGTTGA...

Protein

Download Protein FASTA

429 aa · LXL04_022280|LXL04_022280|OH1004|PROTEIN

MAAAATRFFSLFESNATSTATTAANLYPFRAIRLQPTLFCSPTLRFRRYSSSSAAVIENDSPTTATLGETTEASHQHPWPEWVTFVDRLKTKGYLNKEGGNDVAVYKDMTILKEACLSFGRDRFDIFKSLSMQDIQTLVDKGCPNINRKTVNSGKRLRAHLQLVEGDVCGACILRGSCDRAFVILKDIESGARTVDIVRILLNYALDPVTVSNSKPSGAEIVEKSAKKLLLELTELSDTAIEPELQKPPATIPKKVQSFE...

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_022280`
TK1151 ID	TkA05G455970
OH-1004 ID	LXL04_022280
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_022280

Location Chr04:147500200-147502144 (-)

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_022280 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0001975 response to amphetamine Biological Process

GO:0002224 toll-like receptor signaling pathway Biological Process

GO:0002753 cytoplasmic pattern recognition receptor signaling pathway Biological Process

GO:0006111 regulation of gluconeogenesis Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006457 protein folding Biological Process

GO:0006607 NLS-bearing protein import into nucleus Biological Process

GO:0006913 nucleocytoplasmic transport Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0016925 protein sumoylation Biological Process

GO:0045824 negative regulation of innate immune response Biological Process

KEGG gene cross-reference

ath:AT5G17790

mmu:19386

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.

Plastid0.655

Rank 1 · LXL04_022280 · OH-1004

Mitochondrion0.217

Rank 2 · LXL04_022280 · OH-1004

Nucleus0.156

Rank 3 · LXL04_022280 · OH-1004

Cytoplasm0.081

Rank 4 · LXL04_022280 · OH-1004

Cell membrane0.027

Rank 5 · LXL04_022280 · 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.

PF00641.24Zn_ribbon_RanBP312-340 aa

PF00641.24Zn_ribbon_RanBP351-374 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022280	`PF00641.24`	Zn_ribbon_RanBP	312	340	5.9e-23	80.5
LXL04_022280	`PF00641.24`	Zn_ribbon_RanBP	351	374	5.9e-23	80.5

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	28.571%	Swiss-Prot	weak database homology

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