LXL04_009016 | RubberDandelionOmics

Gene overview

LXL04_009016

Reference: OH-1004 Chr: Chr02 Coordinates: 116219150-116219491 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

342 bp · LXL04_009016|LXL04_009016|OH1004|cDNA

atggaAGGTGACATATTTTCTGGAATTGGAAACGGGTCACAAATAGGAGTAGATGGGAAAGTACTACAAACATTTCAAAAGAGCTTTGTTCAAGTCCAAAACATTTTGGATCAAAACAGACTGCTGATCAACGAAATCAACCAGAATCAAGAATCAAAATTACCCGTAAATCTGACAAGAAACGTGGGTCTAATCAGAGAACTCAACAACAATGTTAAAAGAGTTGTTGATCTTTATGGCGATCTTTCAAGCTCTTTTAG...

CDS

Download CDS FASTA

342 bp · LXL04_009016|LXL04_009016|OH1004|CDS

ATGGAAGGTGACATATTTTCTGGAATTGGAAACGGGTCACAAATAGGAGTAGATGGGAAAGTACTACAAACATTTCAAAAGAGCTTTGTTCAAGTCCAAAACATTTTGGATCAAAACAGACTGCTGATCAACGAAATCAACCAGAATCAAGAATCAAAATTACCCGTAAATCTGACAAGAAACGTGGGTCTAATCAGAGAACTCAACAACAATGTTAAAAGAGTTGTTGATCTTTATGGCGATCTTTCAAGCTCTTTTAG...

Protein

Download Protein FASTA

113 aa · LXL04_009016|LXL04_009016|OH1004|PROTEIN

MEGDIFSGIGNGSQIGVDGKVLQTFQKSFVQVQNILDQNRLLINEINQNQESKLPVNLTRNVGLIRELNNNVKRVVDLYGDLSSSFSKSMDASSEAESGGTTRSDGKKRGRSG

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_009016`
TK1151 ID	TkA03G393160
OH-1004 ID	LXL04_009016
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_009016

Location Chr02:116219150-116219491 (+)

Description Similar to EFL4: Protein ELF4-LIKE 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g17455`	Component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.	No verified direct reference in this release
`At1g72630`	Component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.	No verified direct reference in this release
`At2g06255`	Component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.	No verified direct reference in this release
`At2g40080`	Component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.	The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana.2002 · DOI: 10.1038/nature00954 HUA2 is required for the expression of floral repressors in Arabidopsis thaliana.2005 · DOI: 10.1111/j.1365-313x.2004.02300.x ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY.2005 · DOI: 10.1111/j.1365-313x.2005.02531.x ELF4 is required for oscillatory properties of the circadian clock.2007 · DOI: 10.1104/pp.107.096206 Integrating ELF4 into the circadian system through combined structural and functional studies.2009 · DOI: 10.2976/1.3218766 EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock.2012 · DOI: 10.1105/tpc.111.093807
`At2g29950`	Component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.	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_009016 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009648 photoperiodism Biological Process

GO:0009649 entrainment of circadian clock Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010017 red or far-red light signaling pathway Biological Process

GO:0010114 response to red light Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0042753 positive regulation of circadian rhythm Biological Process

GO:0048511 rhythmic process Biological Process

GO:0048573 photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT1G17455

ath:AT1G72630

ath:AT2G06255

ath:AT2G29950

ath:AT2G40080

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.

Nucleus0.719

Rank 1 · LXL04_009016 · OH-1004

Cytoplasm0.375

Rank 2 · LXL04_009016 · OH-1004

Mitochondrion0.030

Rank 3 · LXL04_009016 · OH-1004

Lysosome / Vacuole0.028

Rank 4 · LXL04_009016 · OH-1004

Cell membrane0.026

Rank 5 · LXL04_009016 · 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.

PF07011.17Elf417-97 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009016	`PF07011.17`	Elf4	17	97	6.2e-38	129.3

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
`Q570U6`	Arabidopsis thaliana	Protein ELF4-LIKE 4	69.828%	Swiss-Prot	strong database homology
`Q94BS8`	Arabidopsis thaliana	Protein ELF4-LIKE 2	69.231%	Swiss-Prot	strong database homology
`Q8S8F5`	Arabidopsis thaliana	Protein ELF4-LIKE 3	73.469%	Swiss-Prot	strong database homology
`O04211`	Arabidopsis thaliana	Protein EARLY FLOWERING 4	40.506%	Swiss-Prot	moderate database homology
`O80877`	Arabidopsis thaliana	Protein ELF4-LIKE 1	45.946%	Swiss-Prot	moderate database homology

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