TkA03G396930 | RubberDandelionOmics

Gene overview

TkA03G396930

Reference: TK1151 Chr: Chr03 Coordinates: 98632271-98637086 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1386 bp · TkA03G396930|TK1151|cDNA

ATGGAAGGTGTTGAAGTAACGGCGATACAATCAATCCGTGGTCTTGAAGTAACGGCTATACCATCAACAGGAGATAGGACATCGGAGGATTTCATGGAAGATAATCATCCGATTTCATGGAAGGGGAAGTATAACCGGGATACAATCAATTCAGAGGATACGAGAATGAGCAATGGAACTGGAACTGAGACAACAAGCATCAAACACCAGAGGCGGTGCTCAGCTCCGGTTGTGGCGGTGGTGGTGGTGGTGGTACCGTT...

CDS

Download CDS FASTA

1386 bp · TkA03G396930|TK1151|CDS

ATGGAAGGTGTTGAAGTAACGGCGATACAATCAATCCGTGGTCTTGAAGTAACGGCTATACCATCAACAGGAGATAGGACATCGGAGGATTTCATGGAAGATAATCATCCGATTTCATGGAAGGGGAAGTATAACCGGGATACAATCAATTCAGAGGATACGAGAATGAGCAATGGAACTGGAACTGAGACAACAAGCATCAAACACCAGAGGCGGTGCTCAGCTCCGGTTGTGGCGGTGGTGGTGGTGGTGGTACCGTT...

Protein

Download Protein FASTA

461 aa · TkA03G396930|TK1151|PROTEIN

MEGVEVTAIQSIRGLEVTAIPSTGDRTSEDFMEDNHPISWKGKYNRDTINSEDTRMSNGTGTETTSIKHQRRCSAPVVAVVVVVVPLMSMSVAAGADDIHLSVQNPLSRIHVQHPHQQISFCNPPVSNQNLPMFMIPPRQTIKSEVVNTHTIPQGVIKTEEVYGPSFGLLPYSIAKRNKKLKASKLRNQEPNPDSGENLVAACRYDSSLGLLTKKFVNLIHADKDGILDLNKAAVVLEVQKRRIYDITNVLEGIGLVEKA...

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	`TkA03G396930`
TK1151 ID	TkA03G396930
OH-1004 ID	LXL04_009082
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.800
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 TkA03G396930

Location Chr03:98632271-98637086 (+)

Description Similar to E2FC: Transcription factor E2FC

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g47870`	Involved in transcriptional repression.	The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants.2002 · DOI: 10.1074/jbc.m110616200 Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation.2002 · DOI: 10.1104/pp.010642 Arabidopsis E2Fc functions in cell division and is degraded by the ubiquitin-SCF(AtSKP2) pathway in response to light.2002 · DOI: 10.1105/tpc.006791 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 Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc.2009 · DOI: 10.1007/s11103-009-9527-5
`At5g22220`	May bind target-gene promoters and regulate transcription of cell-cycle and DNA-replication genes.	Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities.2001 · DOI: 10.1023/a:1011848528377 The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants.2002 · DOI: 10.1074/jbc.m110616200 Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation.2002 · DOI: 10.1104/pp.010642 The role of the Arabidopsis E2FB transcription factor in regulating auxin-dependent cell division.2005 · DOI: 10.1105/tpc.105.033761 Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development.2006 · DOI: 10.1104/pp.106.077990
`At2g36010`	Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication.	Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities.2001 · DOI: 10.1023/a:1011848528377 The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants.2002 · DOI: 10.1074/jbc.m110616200 Control of proliferation, endoreduplication and differentiation by the Arabidopsis E2Fa-DPa transcription factor.2002 · DOI: 10.1093/emboj/21.6.1360 Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation.2002 · DOI: 10.1104/pp.010642 Constitutive E2F expression in tobacco plants exhibits altered cell cycle control and morphological change in a cell type-specific manner.2003 · DOI: 10.1104/pp.103.025080 The plant-specific cyclin-dependent kinase CDKB1;1 and transcription factor E2Fa-DPa control the balance of mitotically dividing and endoreduplicating cells in Arabidopsis.2004 · DOI: 10.1105/tpc.104.024398 Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development.2006 · DOI: 10.1104/pp.106.077990 Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc.2009 · DOI: 10.1007/s11103-009-9527-5

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009082 · 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:0000082 G1/S transition of mitotic cell cycle Biological Process

GO:0000902 cell morphogenesis Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006606 protein import into nucleus Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009733 response to auxin Biological Process

GO:0010090 trichome morphogenesis Biological Process

GO:0012501 programmed cell death Biological Process

GO:0019760 glucosinolate metabolic process Biological Process

GO:0042023 DNA endoreduplication Biological Process

KEGG gene cross-reference

ath:AT1G47870

ath:AT2G36010

ath:AT5G22220

mmu:13557

mmu:242705

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.

Nucleus0.926

Rank 1 · TkA03G396930 · TK1151

Cytoplasm0.186

Rank 2 · TkA03G396930 · TK1151

Cell membrane0.021

Rank 3 · TkA03G396930 · TK1151

Mitochondrion0.020

Rank 4 · TkA03G396930 · TK1151

Endoplasmic reticulum0.011

Rank 5 · TkA03G396930 · 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.

PF02319WHD_E2F_TDP206-268 aa

PF01978TrmB236-263 aa

PF01920Prefoldin_2247-314 aa

PF10779XhlA250-265 aa

PF23203KIF21A264-318 aa

PF06698DUF1192271-297 aa

PF25450Rab11-FIP3276-314 aa

PF28968PMD1-like276-317 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G396930	`PF02319`	WHD_E2F_TDP	206	268	3.6e-26	91.4
TkA03G396930	`PF01978`	TrmB	236	263	0.16	12.5
TkA03G396930	`PF01920`	Prefoldin_2	247	314	0.18	12.5
TkA03G396930	`PF10779`	XhlA	250	265	2.2	9.3
TkA03G396930	`PF23203`	KIF21A	264	318	0.044	14.3
TkA03G396930	`PF06698`	DUF1192	271	297	0.031	15.1
TkA03G396930	`PF25450`	Rab11-FIP3	276	314	0.0067	17.4
TkA03G396930	`PF28968`	PMD1-like	276	317	0.038	14.2
TkA03G396930	`PF10018`	Med4	277	314	0.16	12.4
TkA03G396930	`PF10779`	XhlA	278	315	2.2	9.3
TkA03G396930	`PF13747`	DUF4164	279	327	0.17	13.1
TkA03G396930	`PF16421`	E2F_CC-MB	285	385	9.4e-27	93.7
TkA03G396930	`PF10157`	BORCS6	297	312	0.036	14.9
TkA03G396930	`PF06698`	DUF1192	374	386	0.031	15.1
TkA03G396930	`PF10157`	BORCS6	377	428	0.036	14.9

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
`Q9FV70`	Arabidopsis thaliana	sp\|Q9FV70\|E2FC_ARATH Transcription factor E2FC	45.400%	Swiss-Prot	Medium
`Q9FV71`	Arabidopsis thaliana	sp\|Q9FV71\|E2FB_ARATH Transcription factor E2FB	44.100%	Swiss-Prot	Medium
`Q9FNY0`	Arabidopsis thaliana	sp\|Q9FNY0\|E2FA_ARATH Transcription factor E2FA	47.000%	Swiss-Prot	Medium

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