LXL04_002216 | RubberDandelionOmics

Gene overview

LXL04_002216

Reference: OH-1004 Chr: Chr01 Coordinates: 43860040-43871735 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4368 bp · LXL04_002216|LXL04_002216|OH1004|cDNA

ATGAAGAATTCATTCTTCATTGCTCAATTTATAGAACGAAGCGGCGTCTGCCTGCCGCTGGACTTTGCCGCTGCAGGCGGCCGTTCCGTGGAGTTTACCAGCAGCAAACGTTGCCATCTGGCTTGCCGTCGGCTATCGGGTGAGGGTGTGAACGGGGACCGATATGGCATTCGAGAACGTCGTTCTCCGACGTTGCACACCGCCTGGCGTTCTTGCCCATCGCCAATGAAACGACGAGGCGGGCGTTCTTGGCCGTCATT...

CDS

Download CDS FASTA

4368 bp · LXL04_002216|LXL04_002216|OH1004|CDS

ATGAAGAATTCATTCTTCATTGCTCAATTTATAGAACGAAGCGGCGTCTGCCTGCCGCTGGACTTTGCCGCTGCAGGCGGCCGTTCCGTGGAGTTTACCAGCAGCAAACGTTGCCATCTGGCTTGCCGTCGGCTATCGGGTGAGGGTGTGAACGGGGACCGATATGGCATTCGAGAACGTCGTTCTCCGACGTTGCACACCGCCTGGCGTTCTTGCCCATCGCCAATGAAACGACGAGGCGGGCGTTCTTGGCCGTCATT...

Protein

Download Protein FASTA

1455 aa · LXL04_002216|LXL04_002216|OH1004|PROTEIN

MKNSFFIAQFIERSGVCLPLDFAAAGGRSVEFTSSKRCHLACRRLSGEGVNGDRYGIRERRSPTLHTAWRSCPSPMKRRGGRSWPSFESFHHRISLLPRTLCLPSVLFVSLCMNLKDMEAGTGNVASFLKRNQRSVTEIEDLYITLTKMELDMPLDYAAFQLSPKHSRCELIVSSNGNTEKLASGLVKPFSTHLKVVEEQVGSSVQSIKLEVDKRKNVDSWFTKGTLERFVRFVSTPEIVELVITFDAEMSQLEAARKIY...

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_002216`
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_002216

Location Chr01:43860040-43871735 (-)

Description Similar to SEC22: 25.3 kDa vesicle transport protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g11890`	V-SNARE involved in vesicle trafficking from the ER to the Golgi complex and required for early secretion.	Arabidopsis SNARE protein SEC22 is essential for gametophyte development and maintenance of Golgi-stack integrity.2011 · DOI: 10.1111/j.1365-313x.2011.04487.x Caesium accumulation in yeast and plants is selectively repressed by loss of the SNARE Sec22p/SEC22.2013 · DOI: 10.1038/ncomms3092

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002216 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Biological Process

GO:0006906 vesicle fusion Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0007030 Golgi organization Biological Process

GO:0009267 cellular response to starvation Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009555 pollen development Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0016236 macroautophagy Biological Process

GO:0045732 positive regulation of protein catabolic process Biological Process

KEGG gene cross-reference

ath:AT1G11890

hsa:9554

mmu:20333

pon:100172644

rno:310710

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.

Cell membrane0.362

Rank 1 · LXL04_002216 · OH-1004

Cytoplasm0.318

Rank 2 · LXL04_002216 · OH-1004

Nucleus0.281

Rank 3 · LXL04_002216 · OH-1004

Endoplasmic reticulum0.102

Rank 4 · LXL04_002216 · OH-1004

Golgi apparatus0.079

Rank 5 · LXL04_002216 · 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.

PF30469.1CIP7_N157-213 aa

PF30468.1CIP7_M266-349 aa

PF13774.14Longin1266-1357 aa

PF00957.28Synaptobrevin1373-1450 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002216	`PF30469.1`	CIP7_N	157	213	2.7e-25	89.1
LXL04_002216	`PF30468.1`	CIP7_M	266	349	2.7e-17	63.9
LXL04_002216	`PF13774.14`	Longin	1266	1357	3.8e-29	101.5
LXL04_002216	`PF00957.28`	Synaptobrevin	1373	1450	1.7e-17	63.8

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
`Q94AU2`	Arabidopsis thaliana	25.3 kDa vesicle transport protein SEC22-1	86.697%	Swiss-Prot	weak database homology

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