LXL04_027869 | RubberDandelionOmics

Gene overview

LXL04_027869

Reference: OH-1004 Chr: Chr06 Coordinates: 25079759-25087922 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3654 bp · LXL04_027869|LXL04_027869|OH1004|cDNA

ATGGGGATCCAGACTAACTCATCCGATCTTGCAGAAGACGATCTTGCGGAAGACGACCACCTTCTTCGTCATCTGAGTCGTCACTTGAcggtgtttgatactgtggtgacggtgtttgatactgtggtGGCGCTGTTTGATACTGTGGTAgcggtgtttgatactgtggtagcggtgtttgatactgtggtAGAGGTGACTGATACTGCGGTGTTTAATACTGTGTTTGCAACCATGTTTGAAACAtttgctgttgttgc...

CDS

Download CDS FASTA

3654 bp · LXL04_027869|LXL04_027869|OH1004|CDS

ATGGGGATCCAGACTAACTCATCCGATCTTGCAGAAGACGATCTTGCGGAAGACGACCACCTTCTTCGTCATCTGAGTCGTCACTTGACGGTGTTTGATACTGTGGTGACGGTGTTTGATACTGTGGTGGCGCTGTTTGATACTGTGGTAGCGGTGTTTGATACTGTGGTAGCGGTGTTTGATACTGTGGTAGAGGTGACTGATACTGCGGTGTTTAATACTGTGTTTGCAACCATGTTTGAAACATTTGCTGTTGTTGC...

Protein

Download Protein FASTA

1217 aa · LXL04_027869|LXL04_027869|OH1004|PROTEIN

MGIQTNSSDLAEDDLAEDDHLLRHLSRHLTVFDTVVTVFDTVVALFDTVVAVFDTVVAVFDTVVEVTDTAVFNTVFATMFETFAVVAVAEDQMSGCIPLVAEGYLRGIAAGRLPLIPFGLWILQVLSSPKWENSYCCGVCSSIDRSMATPGGPRPGNLPPNYNPNSIANNMQNLQTNRPNQPPNSGGGPRGPPPPFGQQPRPQSQPQSQPYSSSPFPGATQSGPSPPGAVPRGVMQMQPPSGPPQAALPPFMAANRPTGG...

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_027869`
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_027869

Location Chr06:25079759-25087922 (-)

Description Similar to At4g32640: Protein transport protein Sec24-like At4g32640

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g32640`	Component of the coat protein complex II (COPII), that covers ER-derived vesicles involved in transport from the endoplasmic reticulum to the Golgi apparatus.	No verified direct reference in this release
`At3g44340`	Component of the coat protein complex II (COPII), that covers ER-derived vesicles involved in transport from the endoplasmic reticulum to the Golgi apparatus.	No verified direct reference in this release
`At3g07100`	Essential protein.	A missense mutation in the Arabidopsis COPII coat protein Sec24A induces the formation of clusters of the endoplasmic reticulum and Golgi apparatus.2009 · DOI: 10.1105/tpc.109.068262 Evidence for the involvement of the Arabidopsis SEC24A in male transmission.2011 · DOI: 10.1093/jxb/err174 Endomembrane trafficking protein SEC24A regulates cell size patterning in Arabidopsis.2014 · DOI: 10.1104/pp.114.246033 The Vesicle-Forming 6K2 Protein of Turnip Mosaic Virus Interacts with the COPII Coatomer Sec24a for Viral Systemic Infection.2015 · DOI: 10.1128/jvi.00503-15

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_027869 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

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

GO:0006979 response to oxidative stress Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0007030 Golgi organization Biological Process

GO:0008361 regulation of cell size Biological Process

GO:0009555 pollen development Biological Process

GO:0032876 negative regulation of DNA endoreduplication Biological Process

GO:0046740 transport of virus in host, cell to cell Biological Process

GO:0048232 male gamete generation Biological Process

GO:0070863 positive regulation of protein exit from endoplasmic reticulum Biological Process

GO:0080119 ER body organization Biological Process

KEGG gene cross-reference

ath:AT3G07100

ath:AT3G44340

ath:AT4G32640

hsa:9632

hsa:9871

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.

Cytoplasm0.664

Rank 1 · LXL04_027869 · OH-1004

Golgi apparatus0.202

Rank 2 · LXL04_027869 · OH-1004

Nucleus0.173

Rank 3 · LXL04_027869 · OH-1004

Lysosome / Vacuole0.115

Rank 4 · LXL04_027869 · OH-1004

Cell membrane0.106

Rank 5 · LXL04_027869 · 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.

PF04810.21zf-Sec23_Sec24552-590 aa

PF04811.22Sec23_trunk627-867 aa

PF08033.18Sec23_BS872-956 aa

PF04815.21Sec23_helical967-1061 aa

PF00626.28Gelsolin1088-1158 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027869	`PF04810.21`	zf-Sec23_Sec24	552	590	5.3e-17	62.3
LXL04_027869	`PF04811.22`	Sec23_trunk	627	867	2.1e-72	244.3
LXL04_027869	`PF08033.18`	Sec23_BS	872	956	6.3e-27	94.7
LXL04_027869	`PF04815.21`	Sec23_helical	967	1061	8.6e-24	84.0
LXL04_027869	`PF00626.28`	Gelsolin	1088	1158	1.7e-07	31.6

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
`Q9M081`	Arabidopsis thaliana	Protein transport protein SEC24 C	63.354%	Swiss-Prot	strong database homology
`Q9M291`	Arabidopsis thaliana	Protein transport protein SEC24 B	72.922%	Swiss-Prot	moderate database homology
`Q9SFU0`	Arabidopsis thaliana	Protein transport protein SEC24 A	31.771%	Swiss-Prot	moderate database homology

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