LXL04_004811 | RubberDandelionOmics

Gene overview

LXL04_004811

Reference: OH-1004 Chr: Chr01 Coordinates: 147231561-147234461 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1431 bp · LXL04_004811|LXL04_004811|OH1004|cDNA

ATGTCTGAAGCTCGAGCTGCAAACCGCCAGGCGGCGCAACCACCACCGCAAGCATCGGTTGGcggtggaggaggaggaggacagaTCCTTAATCCAATGAGGCGTCACTTACCTTTCTCCTCGACTAGACCGCCGTTTATTCCGCCCGACGACTACCACCGTTTTTCGTCCCCAAATAATGGTAATAGAGTCGCCACCACCGCCGATCAGGAAACTGAAGTCCTTATAGTTAAATCTCCGCCAGTAAAAAGAAAGCTTGG...

CDS

Download CDS FASTA

1431 bp · LXL04_004811|LXL04_004811|OH1004|CDS

ATGTCTGAAGCTCGAGCTGCAAACCGCCAGGCGGCGCAACCACCACCGCAAGCATCGGTTGGCGGTGGAGGAGGAGGAGGACAGATCCTTAATCCAATGAGGCGTCACTTACCTTTCTCCTCGACTAGACCGCCGTTTATTCCGCCCGACGACTACCACCGTTTTTCGTCCCCAAATAATGGTAATAGAGTCGCCACCACCGCCGATCAGGAAACTGAAGTCCTTATAGTTAAATCTCCGCCAGTAAAAAGAAAGCTTGG...

Protein

Download Protein FASTA

476 aa · LXL04_004811|LXL04_004811|OH1004|PROTEIN

MSEARAANRQAAQPPPQASVGGGGGGGQILNPMRRHLPFSSTRPPFIPPDDYHRFSSPNNGNRVATTADQETEVLIVKSPPVKRKLGTDYNGVSSNDWGSIGYTTTANSPLHTPVSAKGTRVNGRSKVTKSNKSAPQTPVSNTGSPAPLTPVGSCRYDSSLGLLTKKFINLIKHAEDGILDLNNAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDSSKPGELEDDVALLQAEVQKLTMEEHKLDENIREMQE...

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	`LXL04_004811`
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004811

Location Chr01:147231561-147234461 (-)

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.

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.

Nucleus0.952

Rank 1 · LXL04_004811 · OH-1004

Cytoplasm0.185

Rank 2 · LXL04_004811 · OH-1004

Mitochondrion0.019

Rank 3 · LXL04_004811 · OH-1004

Cell membrane0.018

Rank 4 · LXL04_004811 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_004811 · OH-1004

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.

PF02319.27WHD_E2F_TDP158-221 aa

PF16421.11E2F_CC-MB237-337 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004811	`PF02319.27`	WHD_E2F_TDP	158	221	3.4e-27	94.7
LXL04_004811	`PF16421.11`	E2F_CC-MB	237	337	4.6e-35	120.4

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
`Q9FNY0`	Arabidopsis thaliana	Transcription factor E2FA	56.223%	Swiss-Prot	strong database homology
`Q9FV71`	Arabidopsis thaliana	Transcription factor E2FB	54.699%	Swiss-Prot	strong database homology
`Q9FV70`	Arabidopsis thaliana	Transcription factor E2FC	47.039%	Swiss-Prot	moderate database homology

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