TkA04G474470 | RubberDandelionOmics

Gene overview

TkA04G474470

Reference: TK1151 Chr: Chr04 Coordinates: 119816640-119818011 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1180 bp · TkA04G474470|TK1151|cDNA

TTTAAATCCACTTGGTCTCACTCACTATATAGTTTCCTTTAAAACCCAATCCACATCCACACACAACTCCCGCTTCCATTCCATCTTCATCGGGAAATCAAGAAATCTTGAAACCCAAAAATGGCCACCCAATTGAACGTTTTGCCGGAAGACTGTATTTCCAGTATATTTTCTCTCACATCTGCGGCAGATGCATGTAGATTAATGCTTGCATCTTCTTCGTTGAGATCAGCTGCCGAGTCCGACATGGTGTGGGGAAG...

CDS

Download CDS FASTA

837 bp · TkA04G474470|TK1151|CDS

ATGGCCACCCAATTGAACGTTTTGCCGGAAGACTGTATTTCCAGTATATTTTCTCTCACATCTGCGGCAGATGCATGTAGATTAATGCTTGCATCTTCTTCGTTGAGATCAGCTGCCGAGTCCGACATGGTGTGGGGAAGATTCTTGCCATCTGATCTCCCTTCGATTCTATCAAGAACACATTCTCAATTAAACTTTTCTTCCATGAAAGAACTCTATTTCCAGCTCTGTGATTCCGTTCTCATTGATGATGGATATAG...

Protein

Download Protein FASTA

278 aa · TkA04G474470|TK1151|PROTEIN

MATQLNVLPEDCISSIFSLTSAADACRLMLASSSLRSAAESDMVWGRFLPSDLPSILSRTHSQLNFSSMKELYFQLCDSVLIDDGYRSFSLNKISGKKSFFLSSGALSISLSNEPNHWTWSTHSASRFSEVIELKSIPSIEIEGKINTQDLTPNTKYGAYLVMQVSDRAFGLDSIASEISVSKDECSVSNTAYLCPVNERKQQLESLLFMNRRRMMEKLVVEGEGRRPIKRDDGWMEIELGEFFVGEKSEEVIMTLMEIK...

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	`TkA04G474470`
TK1151 ID	TkA04G474470
OH-1004 ID	LXL04_038884
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	84.500
Protein coverage (%)	TK1151 100.000 / OH-1004 99.642 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 TkA04G474470

Location Chr04:119816640-119818011 (-)

Description Similar to VBF: F-box protein VBF

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g56250`	Component of SCF(VBF) E3 ubiquitin ligase complexes, which mediate the ubiquitination and subsequent proteasomal degradation of target proteins such as VIP1 and Agrobacterium virE2, after their implication in T-DNA translocation to the host nucleus (can functionally replace Agrobacterium VirF).	No verified direct reference in this release
`At1g56240`	F-box protein PP2-B13.	No verified direct reference in this release
`At1g09155`	F-box protein PP2-B15.	No verified direct reference in this release
`At2g02240`	F-box protein At2g02240.	No verified direct reference in this release
`At2g02250`	Putative F-box protein PP2-B2.	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_038884 · 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:0009617 response to bacterium Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0030246 carbohydrate binding Molecular Function

KEGG gene cross-reference

ath:AT1G09155

ath:AT1G56240

ath:AT1G56250

ath:AT2G02240

ath:AT2G02250

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.

Nucleus0.640

Rank 1 · TkA04G474470 · TK1151

Cytoplasm0.496

Rank 2 · TkA04G474470 · TK1151

Endoplasmic reticulum0.057

Rank 3 · TkA04G474470 · TK1151

Cell membrane0.049

Rank 4 · TkA04G474470 · TK1151

Lysosome / Vacuole0.025

Rank 5 · TkA04G474470 · 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.

PF12937F-box-like6-48 aa

PF00646F-box8-45 aa

PF12374Dmrt121-62 aa

PF14299PP297-277 aa

PF12374Dmrt1115-140 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G474470	`PF12937`	F-box-like	6	48	3.6e-06	27.3
TkA04G474470	`PF00646`	F-box	8	45	3.8e-05	24.1
TkA04G474470	`PF12374`	Dmrt1	21	62	0.56	11.4
TkA04G474470	`PF14299`	PP2	97	277	4.5e-46	157.2
TkA04G474470	`PF12374`	Dmrt1	115	140	0.56	11.4

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
`Q9C7K0`	Arabidopsis thaliana	sp\|Q9C7K0\|VBF_ARATH F-box protein VBF	49.100%	Swiss-Prot	Medium
`Q9C7J9`	Arabidopsis thaliana	sp\|Q9C7J9\|P2B13_ARATH F-box protein PP2-B13	49.100%	Swiss-Prot	Medium
`O80494`	Arabidopsis thaliana	sp\|O80494\|P2B15_ARATH F-box protein PP2-B15	47.500%	Swiss-Prot	Medium
`Q3E6P4`	Arabidopsis thaliana	sp\|Q3E6P4\|FB95_ARATH F-box protein At2g02240	40.100%	Swiss-Prot	Medium
`Q9ZVR5`	Arabidopsis thaliana	sp\|Q9ZVR5\|PP2B2_ARATH Putative F-box protein PP2-B2	39.100%	Swiss-Prot	Medium

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