TkA01G109400 | RubberDandelionOmics

Gene overview

TkA01G109400

Reference: TK1151 Chr: Chr01 Coordinates: 27774582-27777973 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1936 bp · TkA01G109400|TK1151|cDNA

CGAACCAAAAATTCCCTCCTTCCCTCGTTTTCTGCTCTCCCTAATCAAACCCCCACTTTCTCTTCCAAACCCTTGCTTTCTCTCTCTAAAACAAACCCTCCATTTTCACAGATCCCTCGCCTTCTCTCTCTAAAACCCCCAAACCTCCCTTCGTTCTTCTATATTATTCTAAACCCTAAACTCAATTTAGTTATATCGATTACAAAAGTTTCTATTTTAAATTTGGTATACTTTTTGGTACAAAATGTCTGAAGCTCGAG...

CDS

Download CDS FASTA

1425 bp · TkA01G109400|TK1151|CDS

ATGTCTGAAGCTCGAGCTGCAAACCGCCAGGCGGCGCAACCACCACCGCAAGCATCGGTTGGCGGTGGAGGAGGAGGAGGACAGATCCTTCATCCAATGAGGCGTCACTTACCTTTCTCCTCGACTAGACCGCCGTTTATTCCGCCCGACGACTACCACCGTTTTTCGTCCCCAAATAATGGTAATAGAGTCGCCACCACCGCCGATCAGGAAACTGAAGTTCTTATAGTTAAATCTCCGCCAGTAAAAAGAAAGCTTGG...

Protein

Download Protein FASTA

474 aa · TkA01G109400|TK1151|PROTEIN

MSEARAANRQAAQPPPQASVGGGGGGGQILHPMRRHLPFSSTRPPFIPPDDYHRFSSPNNGNRVATTADQETEVLIVKSPPVKRKLGTDYNGVSSNDWGSIGYTTTANSPLHTPVSAKGTRVNGRSKVTKSNKSAPQTPVSNTGSPAPLTPVGSCRYDSSLGLLTKKFINLIKHAEDGILDLNNAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDSSKPGELEDDVALLQAEVQKLTMEEHKLDENIREMQE...

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	`TkA01G109400`
TK1151 ID	TkA01G109400
OH-1004 ID	LXL04_004811
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.500
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G109400

Location Chr01:27774582-27777973 (+)

Description Similar to E2FA: Transcription factor E2FA

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004811 · 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:0030030 cell projection organization Biological Process

KEGG gene cross-reference

ath:AT1G47870

ath:AT2G36010

ath:AT5G22220

mmu:13557

mmu:13559

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.

Nucleus0.950

Rank 1 · TkA01G109400 · TK1151

Cytoplasm0.189

Rank 2 · TkA01G109400 · TK1151

Mitochondrion0.020

Rank 3 · TkA01G109400 · TK1151

Cell membrane0.018

Rank 4 · TkA01G109400 · TK1151

Endoplasmic reticulum0.009

Rank 5 · TkA01G109400 · 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_TDP158-221 aa

PF29209DUF8511170-217 aa

PF01978TrmB186-217 aa

PF10779XhlA202-215 aa

PF29209DUF8511217-260 aa

PF26095CC_Bre1224-269 aa

PF25450Rab11-FIP3228-271 aa

PF04977DivIC229-259 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G109400	`PF02319`	WHD_E2F_TDP	158	221	3.3e-27	94.7
TkA01G109400	`PF29209`	DUF8511	170	217	0.74	10.5
TkA01G109400	`PF01978`	TrmB	186	217	0.13	12.8
TkA01G109400	`PF10779`	XhlA	202	215	2.6	9.1
TkA01G109400	`PF29209`	DUF8511	217	260	0.74	10.5
TkA01G109400	`PF26095`	CC_Bre1	224	269	0.035	15.1
TkA01G109400	`PF25450`	Rab11-FIP3	228	271	0.017	16.2
TkA01G109400	`PF04977`	DivIC	229	259	0.39	11.3
TkA01G109400	`PF06005`	ZapB	232	271	0.028	15.6
TkA01G109400	`PF12329`	TMF_DNA_bd	232	273	0.12	13.1
TkA01G109400	`PF16559`	GIT_CC	232	273	0.86	10.1
TkA01G109400	`PF16421`	E2F_CC-MB	237	337	4.5e-35	120.4
TkA01G109400	`PF10779`	XhlA	237	276	2.6	9.1
TkA01G109400	`PF07160`	SKA1	241	285	0.11	13.1

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
`Q9FNY0`	Arabidopsis thaliana	sp\|Q9FNY0\|E2FA_ARATH Transcription factor E2FA	56.200%	Swiss-Prot	High
`Q9FV71`	Arabidopsis thaliana	sp\|Q9FV71\|E2FB_ARATH Transcription factor E2FB	50.400%	Swiss-Prot	High
`Q9FV70`	Arabidopsis thaliana	sp\|Q9FV70\|E2FC_ARATH Transcription factor E2FC	50.200%	Swiss-Prot	Medium

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