LXL04_003466 | RubberDandelionOmics

Gene overview

LXL04_003466

Reference: OH-1004 Chr: Chr01 Coordinates: 80194310-80196813 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2352 bp · LXL04_003466|LXL04_003466|OH1004|cDNA

ATGGATTTCGTCGAATTGGAAGCCATCGAAGGTCTACGATGGTCATGGAATTCATGGCCAGTATCAAGAACCGATTCAAACGATCTGGTAATCCCTTTGTCCATAATGCAAACTCCATTGATGAAATTCAACGAACTTCCACTCCTATCCTACGATCCACTGATCTGTTCTCGATGTGGCTCCGTCTTAAACCCGTACGCCCGAGTCGATTACCCTTCTCGAATTTGGATTTGCCCGTTTTGTTATCAGAAGAATTCATT...

CDS

Download CDS FASTA

2352 bp · LXL04_003466|LXL04_003466|OH1004|CDS

ATGGATTTCGTCGAATTGGAAGCCATCGAAGGTCTACGATGGTCATGGAATTCATGGCCAGTATCAAGAACCGATTCAAACGATCTGGTAATCCCTTTGTCCATAATGCAAACTCCATTGATGAAATTCAACGAACTTCCACTCCTATCCTACGATCCACTGATCTGTTCTCGATGTGGCTCCGTCTTAAACCCGTACGCCCGAGTCGATTACCCTTCTCGAATTTGGATTTGCCCGTTTTGTTATCAGAAGAATTCATT...

Protein

Download Protein FASTA

783 aa · LXL04_003466|LXL04_003466|OH1004|PROTEIN

MDFVELEAIEGLRWSWNSWPVSRTDSNDLVIPLSIMQTPLMKFNELPLLSYDPLICSRCGSVLNPYARVDYPSRIWICPFCYQKNSFPRSYAEIGENNIPAELFPTYSTVEYQLGHQGLMTPTRMNSNPVHNWGTSNGSGLTKSSSSSFSSSSLSSLDQRGLTGRGLGIGPAFVFVVDASSTEDELQALKNELLLIVAQLPENAMVGLIVFDSMVKVYDLGFTECLRVVVLHGERNPSSTQMIEFLGINPARQQLGKPQT...

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_003466`
TK1151 ID	TkA01G355860
OH-1004 ID	LXL04_003466
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.500
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_003466

Location Chr01:80194310-80196813 (-)

Description Similar to SEC23: Protein transport protein SEC23 (Ustilago maydis (strain 521 / FGSC 9021)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g43670`	Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).	No verified direct reference in this release
`At3g23660`	Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).	No verified direct reference in this release
`At1g05520`	Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER) (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003466 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0090110 COPII-coated vesicle cargo loading Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0030127 COPII vesicle coat Cellular Component

GO:0070971 endoplasmic reticulum exit site Cellular Component

GO:0005096 GTPase activator activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G05520

ath:AT3G23660

ath:AT5G43670

cnb:CNBJ2310

uma:UMAG_01624

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.

Cytoplasm0.620

Rank 1 · LXL04_003466 · OH-1004

Golgi apparatus0.190

Rank 2 · LXL04_003466 · OH-1004

Lysosome / Vacuole0.172

Rank 3 · LXL04_003466 · OH-1004

Nucleus0.167

Rank 4 · LXL04_003466 · OH-1004

Cell membrane0.087

Rank 5 · LXL04_003466 · 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.

PF04810.21zf-Sec23_Sec2453-91 aa

PF04811.22Sec23_trunk171-427 aa

PF08033.18Sec23_BS439-529 aa

PF04815.21Sec23_helical541-637 aa

PF00626.28Gelsolin655-741 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003466	`PF04810.21`	zf-Sec23_Sec24	53	91	6.9e-14	52.3
LXL04_003466	`PF04811.22`	Sec23_trunk	171	427	2.1e-50	172.3
LXL04_003466	`PF08033.18`	Sec23_BS	439	529	1.9e-17	64.3
LXL04_003466	`PF04815.21`	Sec23_helical	541	637	6.6e-23	81.2
LXL04_003466	`PF00626.28`	Gelsolin	655	741	1.9e-07	31.5

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
`Q84WI4`	Arabidopsis thaliana	Protein transport protein SEC23 G	60.050%	Swiss-Prot	strong database homology
`Q9LUG1`	Arabidopsis thaliana	Protein transport protein SEC23 E	42.590%	Swiss-Prot	moderate database homology
`Q8H0S3`	Arabidopsis thaliana	Protein transport protein SEC23 B	41.082%	Swiss-Prot	moderate database homology

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