TkA03G478920 | RubberDandelionOmics

Gene overview

TkA03G478920

Reference: TK1151 Chr: Chr03 Coordinates: 119727456-119729731 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1115 bp · TkA03G478920|TK1151|cDNA

GTGAAATCAAACGCTAATTCACTCCATCTACACCATCTTGAGCGAGAGAGAGCTCTGAAAATGGAGGATTTCGGTGGCGCATTCGGTACGGAAGGAGTGGAGATTCCCGCGGCTACGTCTCAAAACAACGATGGTTACGACACAGGCCAAAACTACGGGCTCGAAAGTTCTATTCCTGCCGATGACCTTAACACCGTACATGACGCTCCTCCTCCGCATCAAGACGAAAAGACGTATTTGCCTGAGAATTATGGAGATTT...

CDS

Download CDS FASTA

906 bp · TkA03G478920|TK1151|CDS

ATGGAGGATTTCGGTGGCGCATTCGGTACGGAAGGAGTGGAGATTCCCGCGGCTACGTCTCAAAACAACGATGGTTACGACACAGGCCAAAACTACGGGCTCGAAAGTTCTATTCCTGCCGATGACCTTAACACCGTACATGACGCTCCTCCTCCGCATCAAGACGAAAAGACGTATTTGCCTGAGAATTATGGAGATTTCTCTTCATCGTCCGCCTTCGAACCGGAATCAAACGGCAATTCTAAGCCGTACGACTTAGG...

Protein

Download Protein FASTA

301 aa · TkA03G478920|TK1151|PROTEIN

MEDFGGAFGTEGVEIPAATSQNNDGYDTGQNYGLESSIPADDLNTVHDAPPPHQDEKTYLPENYGDFSSSSAFEPESNGNSKPYDLGADTEGIFTSSGNGDGGEPLLPEPSQMREEGAAFREWRRQNAINLEEKEKKEREMRNQLIAEADEFKRAFTEKRQKNTESNTALNREREKQYLINQEKFHKEADQQYWKAIAELIPREVAQIDKRRARVDKEEEKKPGIVVIQGPKPGKPTDLSRMRQLCMNLKQNPPSHMLPS...

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	`TkA03G478920`
TK1151 ID	TkA03G478920
OH-1004 ID	LXL04_009856
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G478920

Location Chr03:119727456-119729731 (+)

Description Similar to CLC2: Clathrin light chain 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g20760`	Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.	No verified direct reference in this release
`At2g40060`	Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0731800`	Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.	No verified direct reference in this release
`Os07g0461500`	Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.	No verified direct reference in this release
`Os04g0679100`	Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009856 · 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:0071280 cellular response to copper ion Biological Process

GO:0072583 clathrin-dependent endocytosis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009504 cell plate Cellular Component

GO:0009524 phragmoplast Cellular Component

GO:0009941 chloroplast envelope Cellular Component

KEGG gene cross-reference

ath:AT2G20760

ath:AT2G40060

dosa:Os04g0679100

dosa:Os06g0731800

dosa:Os07g0461500

osa:9267670

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.

Cytoplasm0.724

Rank 1 · TkA03G478920 · TK1151

Nucleus0.190

Rank 2 · TkA03G478920 · TK1151

Golgi apparatus0.162

Rank 3 · TkA03G478920 · TK1151

Cell membrane0.097

Rank 4 · TkA03G478920 · TK1151

Endoplasmic reticulum0.052

Rank 5 · TkA03G478920 · 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.

PF01086Clathrin_lg_ch102-205 aa

PF26815Phage_RepB125-195 aa

PF01086Clathrin_lg_ch231-252 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G478920	`PF01086`	Clathrin_lg_ch	102	205	5.3e-10	40.3
TkA03G478920	`PF26815`	Phage_RepB	125	195	0.27	11.6
TkA03G478920	`PF01086`	Clathrin_lg_ch	231	252	5.3e-10	40.3

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
`Q9SKU1`	Arabidopsis thaliana	sp\|Q9SKU1\|CLC1_ARATH Clathrin light chain 1	62.000%	Swiss-Prot	Medium
`O04209`	Arabidopsis thaliana	sp\|O04209\|CLC2_ARATH Clathrin light chain 2	54.800%	Swiss-Prot	Medium
`Q5Z402`	Oryza sativa subsp. japonica	sp\|Q5Z402\|CLC2_ORYSJ Clathrin light chain 2	68.900%	Swiss-Prot	Low
`Q6Z3A8`	Oryza sativa subsp. japonica	sp\|Q6Z3A8\|CLC3_ORYSJ Clathrin light chain 3	59.500%	Swiss-Prot	Medium
`Q7XKE9`	Oryza sativa subsp. japonica	sp\|Q7XKE9\|CLC1_ORYSJ Clathrin light chain 1	63.800%	Swiss-Prot	Medium

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