TkA03G008880 | RubberDandelionOmics

Gene overview

TkA03G008880

Reference: TK1151 Chr: Chr03 Coordinates: 2168253-2173805 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2536 bp · TkA03G008880|TK1151|cDNA

AAAAATTAGTAAAGAATATTGATGAAGAAACAATATTTGTTACATACCATTAATTTCTTATTTATTTATCTTTCACTATCATACAAAATACTATAATCTATATTCCAAAGGAAGTGTGTGGCCTACAACTCAACTCGAATGATTTCGCACTAAAAAGGATTAAAGAATTTAGCAAGACATTTGGTAGACTTCGTTCATCCCATATTCCCACTCCCACCAATCACCATGTGCAGGGTTCGATAATTCAATTTAACGAAGAC...

CDS

Download CDS FASTA

1416 bp · TkA03G008880|TK1151|CDS

ATGGGGAACAAAAGTTCAAGAGACGAGCGGCCGAGTTACAGGCAGTCGCCATCGTTCCAATCAACATCATCTTTCAGTGGTAGTCCATACGGCAGCTATCCTCAACAATCTTATCCAAATCCGCCTCAAGACATTCATAATTACCCTGTTCAAGAGGCTTATCCAGCTTATCCACAAGATTATCATGCACCCCCACCTGCACCTGCACCTGCACATTCTCAACCCCAAAGACCACAAAAGAGGCTTGACAGGAAGTATTC...

Protein

Download Protein FASTA

471 aa · TkA03G008880|TK1151|PROTEIN

MGNKSSRDERPSYRQSPSFQSTSSFSGSPYGSYPQQSYPNPPQDIHNYPVQEAYPAYPQDYHAPPPAPAPAHSQPQRPQKRLDRKYSRIADNYTSLEQVTEALARAGLESSNLIVGIDFTKSNEWTGSRSFNRKSLHHIGDGLNPYEQAITIIGKTLAAFDEDNLIPCYGFGDASTHDQDVFSFYPEERFCNGFEEVLSRYREIVPHLKLAGPTSFAPVIEQAVTIVEESGGQYHVLLIIADGQVTRSVDTEPGNLSPQE...

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	`TkA03G008880`
TK1151 ID	TkA03G008880
OH-1004 ID	LXL04_023905
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	70.300
Protein coverage (%)	TK1151 99.788 / OH-1004 55.083 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G008880

Location Chr03:2168253-2173805 (-)

Description Similar to RGLG2: E3 ubiquitin-protein ligase RGLG2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g14420`	E3 ubiquitin-protein ligase that mediates the formation of 'Lys-63'-linked ubiquitin chains.	Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis.2007 · DOI: 10.1105/tpc.107.052035 Arabidopsis RGLG2, functioning as a RING E3 ligase, interacts with AtERF53 and negatively regulates the plant drought stress response.2012 · DOI: 10.1104/pp.111.189738
`At3g01650`	E3 ubiquitin-protein ligase that mediates the formation of 'Lys-63'-linked ubiquitin chains.	Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis.2007 · DOI: 10.1105/tpc.107.052035 Arabidopsis RGLG2, functioning as a RING E3 ligase, interacts with AtERF53 and negatively regulates the plant drought stress response.2012 · DOI: 10.1104/pp.111.189738
`At1g67800`	Together with RGLG1, mediates the ubiquitination and subsequent proteasomal degradation of the target protein PP2CA.	No verified direct reference in this release
`At5g63970`	Possesses E3 ubiquitin-protein ligase in vitro.	Two novel RING-type ubiquitin ligases, RGLG3 and RGLG4, are essential for jasmonate-mediated responses in Arabidopsis.2012 · DOI: 10.1104/pp.112.203422 Hijacking of the jasmonate pathway by the mycotoxin fumonisin B1 (FB1) to initiate programmed cell death in Arabidopsis is modulated by RGLG3 and RGLG4.2015 · DOI: 10.1093/jxb/erv068 The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4.2016 · DOI: 10.1093/pcp/pcw122
`At1g79380`	Possesses E3 ubiquitin-protein ligase in vitro.	Two novel RING-type ubiquitin ligases, RGLG3 and RGLG4, are essential for jasmonate-mediated responses in Arabidopsis.2012 · DOI: 10.1104/pp.112.203422 Hijacking of the jasmonate pathway by the mycotoxin fumonisin B1 (FB1) to initiate programmed cell death in Arabidopsis is modulated by RGLG3 and RGLG4.2015 · DOI: 10.1093/jxb/erv068 The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4.2016 · DOI: 10.1093/pcp/pcw122

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023905 · 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:0009690 cytokinin metabolic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009850 auxin metabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0070534 protein K63-linked ubiquitination Biological Process

GO:0080148 negative regulation of response to water deprivation Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G67800

ath:AT3G01650

ath:AT5G14420

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.

Cytoplasm0.623

Rank 1 · TkA03G008880 · TK1151

Nucleus0.365

Rank 2 · TkA03G008880 · TK1151

Cell membrane0.190

Rank 3 · TkA03G008880 · TK1151

Lysosome / Vacuole0.097

Rank 4 · TkA03G008880 · TK1151

Golgi apparatus0.069

Rank 5 · TkA03G008880 · 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.

PF07002Copine135-349 aa

PF10138vWA-TerF-like159-313 aa

PF14447Prok-RING_4424-434 aa

PF13920zf-C3HC4_3425-466 aa

PF13639zf-RING_2427-461 aa

PF24921RING_XB3-XBAT31427-452 aa

PF00097zf-C3HC4428-460 aa

PF13923zf-C3HC4_2428-460 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G008880	`PF07002`	Copine	135	349	3.6e-73	246.4
TkA03G008880	`PF10138`	vWA-TerF-like	159	313	0.00019	22.5
TkA03G008880	`PF14447`	Prok-RING_4	424	434	2.0	9.1
TkA03G008880	`PF13920`	zf-C3HC4_3	425	466	9e-08	32.5
TkA03G008880	`PF13639`	zf-RING_2	427	461	0.48	11.5
TkA03G008880	`PF24921`	RING_XB3-XBAT31	427	452	5.4	7.9
TkA03G008880	`PF00097`	zf-C3HC4	428	460	0.016	15.8
TkA03G008880	`PF13923`	zf-C3HC4_2	428	460	0.28	11.7
TkA03G008880	`PF14447`	Prok-RING_4	428	466	2.0	9.1
TkA03G008880	`PF21362`	Sina_RING	428	460	5.5	7.9
TkA03G008880	`PF24921`	RING_XB3-XBAT31	456	465	5.4	7.9
TkA03G008880	`PF00097`	zf-C3HC4	457	465	0.016	15.8

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
`Q9LY87`	Arabidopsis thaliana	sp\|Q9LY87\|RGLG2_ARATH E3 ubiquitin-protein ligase RGLG2	69.000%	Swiss-Prot	High
`Q9SS90`	Arabidopsis thaliana	sp\|Q9SS90\|RGLG1_ARATH E3 ubiquitin-protein ligase RGLG1	73.000%	Swiss-Prot	High
`Q8LB88`	Arabidopsis thaliana	sp\|Q8LB88\|RGLG5_ARATH E3 ubiquitin-protein ligase RGLG5	66.000%	Swiss-Prot	High
`Q8RX26`	Arabidopsis thaliana	sp\|Q8RX26\|RGLG3_ARATH E3 ubiquitin-protein ligase RGLG3	57.900%	Swiss-Prot	High
`Q9SAL0`	Arabidopsis thaliana	sp\|Q9SAL0\|RGLG4_ARATH E3 ubiquitin-protein ligase RGLG4	54.400%	Swiss-Prot	High

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