TkA08G100810 | RubberDandelionOmics

Gene overview

TkA08G100810

Reference: TK1151 Chr: Chr08 Coordinates: 26150266-26152696 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1856 bp · TkA08G100810|TK1151|cDNA

GCATTTTAGGCATGTGGGGGTCCATAATATTTCCCAAACTTACACAGCCATCCATCCATCAATGACACGTGGTTTCATACGTGTCACCAGTATCTTTCGTTTCGTCACGTTTCCCCCTCCCCGATAAACCTCTCGTGAACTTGGAACAGCTTTTTAGACGACGAAAAGGGGAAAAAAGCACCTTCATTTCTGCCGTACCCACATCAATAATCCAGTACCTTCTTTTTTATTCCATTGCTTCACATAACCTCCAAATTTCC...

CDS

Download CDS FASTA

1053 bp · TkA08G100810|TK1151|CDS

ATGCAAACCGATGAATTGAACATGTATTTCAATAACATGATGGTGCTTGGGGGTGGGAGTCGGGTTATTACAGAGTGGAAGGACATTCCTATGGAACTTTTGATGAGAATCATCTCTTTGTTGGATGATCGGACGGTCATCGTTGCTTCCGGTGTCTGTAGTGGATGGAGGGATGCAATCTGTTGGGGACTTACTCAATTTTCCCTCACTTGGTGCAACAACATGAACAACATGGTACTTTCTCTTGCTCCAAAATTCAC...

Protein

Download Protein FASTA

350 aa · TkA08G100810|TK1151|PROTEIN

MQTDELNMYFNNMMVLGGGSRVITEWKDIPMELLMRIISLLDDRTVIVASGVCSGWRDAICWGLTQFSLTWCNNMNNMVLSLAPKFTKLRVLTLRQSKPQLDDHAVETIAANCHELEDLDLSKSFKLTDWSLYALARGCPNLTKLNISGCSAFSDAALVYLSGFCTKLKILNLCGCVKAASDHALKAIGYKCHQLQSINLGWCEGVSDVGVMSLAYGCPDLRAIDLCGCVLIADESVIALANNCLHLRSLGLYYCQNITD...

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	`TkA08G100810`
TK1151 ID	TkA08G100810
OH-1004 ID	LXL04_031306
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	90.200
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA08G100810

Location Chr08:26150266-26152696 (+)

Description Similar to SKP2B: F-box protein SKP2B

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g21410`	Component of SCF(SKP2A) E3 ubiquitin ligase complexes, which mediate the ubiquitination and subsequent proteasomal degradation of target proteins (including cell cycle repressors).	The balance between cell division and endoreplication depends on E2FC-DPB, transcription factors regulated by the ubiquitin-SCFSKP2A pathway in Arabidopsis.2006 · DOI: 10.1105/tpc.105.039651 SKP2A protein, an F-box that regulates cell division, is degraded via the ubiquitin pathway.2008 · DOI: 10.4161/psb.3.10.5888 The Arabidopsis cell cycle F-box protein SKP2A binds to auxin.2010 · DOI: 10.1105/tpc.110.078972
`At1g77000`	Component of SCF(SKP2B) E3 ubiquitin ligase complexes, which mediate the ubiquitination and subsequent proteasomal degradation of the cyclin-dependent kinase inhibitor KRP1.	Degradation of the cyclin-dependent kinase inhibitor KRP1 is regulated by two different ubiquitin E3 ligases.2008 · DOI: 10.1111/j.1365-313x.2007.03370.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031306 · 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:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0010286 heat acclimation Biological Process

GO:0010311 lateral root formation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0051603 proteolysis involved in protein catabolic process Biological Process

GO:0051781 positive regulation of cell division Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:1901332 negative regulation of lateral root development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G21410

ath:AT1G77000

hsa:84961

mmu:72194

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.440

Rank 1 · TkA08G100810 · TK1151

Cytoplasm0.291

Rank 2 · TkA08G100810 · TK1151

Mitochondrion0.125

Rank 3 · TkA08G100810 · TK1151

Cell membrane0.066

Rank 4 · TkA08G100810 · TK1151

Plastid0.046

Rank 5 · TkA08G100810 · 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-like26-60 aa

PF00646F-box26-61 aa

PF29594LRR_SKP261-135 aa

PF23622LRR_At1g61320_AtMIF162-95 aa

PF13516LRR_664-73 aa

PF24758LRR_At5g5637064-124 aa

PF25013LRR_Zer-164-150 aa

PF23286LRR_1364-95 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G100810	`PF12937`	F-box-like	26	60	3.3e-06	27.5
TkA08G100810	`PF00646`	F-box	26	61	1.5e-05	25.4
TkA08G100810	`PF29594`	LRR_SKP2	61	135	2.2e-24	86.9
TkA08G100810	`PF23622`	LRR_At1g61320_AtMIF1	62	95	1.5	8.9
TkA08G100810	`PF13516`	LRR_6	64	73	1.9e-10	40.7
TkA08G100810	`PF24758`	LRR_At5g56370	64	124	3.3e-07	30.9
TkA08G100810	`PF25013`	LRR_Zer-1	64	150	0.0034	18.3
TkA08G100810	`PF23286`	LRR_13	64	95	0.22	11.9
TkA08G100810	`PF24048`	LRR_NXF1-5	69	130	0.089	13.1
TkA08G100810	`PF12799`	LRR_4	75	101	1.1e-07	32.6
TkA08G100810	`PF23598`	LRR_14	77	189	0.018	14.6
TkA08G100810	`PF29594`	LRR_SKP2	85	277	2.2e-24	86.9
TkA08G100810	`PF25372`	LRR_FBXL15	99	136	9.3e-17	61.3
TkA08G100810	`PF23286`	LRR_13	105	180	0.22	11.9
TkA08G100810	`PF13855`	LRR_8	111	150	0.016	15.6
TkA08G100810	`PF13516`	LRR_6	113	122	1.9e-10	40.7

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
`Q9LPL4`	Arabidopsis thaliana	sp\|Q9LPL4\|SKP2A_ARATH F-box protein SKP2A	75.400%	Swiss-Prot	High
`O49286`	Arabidopsis thaliana	sp\|O49286\|SKP2B_ARATH F-box protein SKP2B	75.300%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card