TkA03G289820 | RubberDandelionOmics

Gene overview

TkA03G289820

Reference: TK1151 Chr: Chr03 Coordinates: 71461343-71466401 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3025 bp · TkA03G289820|TK1151|cDNA

TTTGACCCGTAACTATCGAATTCCTGTGATTCGTATTCCCATGAATGTACAATCAATGAGGCATAATGTACAACCCATAAAAGGAGCCAAGTAACGTAACTAACCTTGCATTCCATGATCGTTGCTTAGGTTTTTCTCACAAACGGTTTTTCAATTAATTTCTTGTTCATCTAAGCTTCATCTTCACTGTTCGATCAGTGGAATTCAACTACATGTATGTCTGGGGAATTGTTTGTGTATCGATTGATTTCATTTAAGGA...

CDS

Download CDS FASTA

1077 bp · TkA03G289820|TK1151|CDS

ATGTTCTTAGTTCCTGACATACATGATGTTTACACTCCTCTCCCCTCTGATTGTATTGTTCAACTTTCTGAGTGTCGTCAGCATCTAGAATCGTTACTGGAAAGCATCCCAACTATTTTTCAAAATAATAAAACGGCTGACTCAGCTTTTGGTGCTGGCATGAAGGGTGCTTTTTTGGCAATGAAGAGTACTGGAGGGAAACTTTTGGTATTTCAATCAGTGTTGCCTTCTGTTGGAATTGGGGCTCTTTCTGGTAGGGA...

Protein

Download Protein FASTA

358 aa · TkA03G289820|TK1151|PROTEIN

MFLVPDIHDVYTPLPSDCIVQLSECRQHLESLLESIPTIFQNNKTADSAFGAGMKGAFLAMKSTGGKLLVFQSVLPSVGIGALSGREAEGRSNISAGEKEPHRLLQPVDKTLKRMAIEFAEYQVFCVFITTQSYVDIASVSVVPRTTGGQVYYYHPFSALSDPAKLYNDLRWNVTRPQGFEAVMRVRCSQGVQVQEYFGNFCKRIPTDIDLPAVDCDKSIMVTLQHDDKLQDGTECSFQCALLYTSIYGERRIRVSTLSL...

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	`TkA03G289820`
TK1151 ID	TkA03G289820
OH-1004 ID	LXL04_027869
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.800
Protein coverage (%)	TK1151 88.268 / OH-1004 26.048 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G289820

Location Chr03:71461343-71466401 (-)

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
`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
`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
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_027869 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Cytoplasm0.535

Rank 1 · TkA03G289820 · TK1151

Golgi apparatus0.296

Rank 2 · TkA03G289820 · TK1151

Endoplasmic reticulum0.149

Rank 3 · TkA03G289820 · TK1151

Nucleus0.149

Rank 4 · TkA03G289820 · TK1151

Lysosome / Vacuole0.131

Rank 5 · TkA03G289820 · TK1151

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.

PF04811Sec23_trunk1-174 aa

PF22052DUF693731-55 aa

PF22052DUF6937149-211 aa

PF08033Sec23_BS179-263 aa

PF04815Sec23_helical274-343 aa

PF08033Sec23_BS285-308 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G289820	`PF04811`	Sec23_trunk	1	174	1e-40	140.6
TkA03G289820	`PF22052`	DUF6937	31	55	0.28	11.2
TkA03G289820	`PF22052`	DUF6937	149	211	0.28	11.2
TkA03G289820	`PF08033`	Sec23_BS	179	263	5.4e-28	98.1
TkA03G289820	`PF04815`	Sec23_helical	274	343	0.0024	18.4
TkA03G289820	`PF08033`	Sec23_BS	285	308	5.4e-28	98.1

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
`Q9M291`	Arabidopsis thaliana	sp\|Q9M291\|SC24B_ARATH Protein transport protein SEC24 B	78.300%	Swiss-Prot	High
`Q9M081`	Arabidopsis thaliana	sp\|Q9M081\|SC24C_ARATH Protein transport protein SEC24 C	74.200%	Swiss-Prot	High
`Q9SFU0`	Arabidopsis thaliana	sp\|Q9SFU0\|SC24A_ARATH Protein transport protein SEC24 A	38.300%	Swiss-Prot	Medium

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