LXL04_025916 | RubberDandelionOmics

Gene overview

LXL04_025916

Reference: OH-1004 Chr: Chr05 Coordinates: 118535309-118541283 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2217 bp · LXL04_025916|LXL04_025916|OH1004|cDNA

atgtgggatacactaacactccccctcagagccggtggctcgatgagtctaaacagggatgtgctgggggtgcgaaacgccggctctgataccatgttaatatatgtggagccccaatattgtctctccaaaagagcccttgtggagagaggggatactccaacatatatagccaattatagatcGCTACCCGGTGTGGGTAGCCGTTCTCGTGAACGCCTCCTACGTGGCCGTCGAAGACGACGTTCTTGGCATTGGAA...

CDS

Download CDS FASTA

2217 bp · LXL04_025916|LXL04_025916|OH1004|CDS

ATGTGGGATACACTAACACTCCCCCTCAGAGCCGGTGGCTCGATGAGTCTAAACAGGGATGTGCTGGGGGTGCGAAACGCCGGCTCTGATACCATGTTAATATATGTGGAGCCCCAATATTGTCTCTCCAAAAGAGCCCTTGTGGAGAGAGGGGATACTCCAACATATATAGCCAATTATAGATCGCTACCCGGTGTGGGTAGCCGTTCTCGTGAACGCCTCCTACGTGGCCGTCGAAGACGACGTTCTTGGCATTGGAA...

Protein

Download Protein FASTA

738 aa · LXL04_025916|LXL04_025916|OH1004|PROTEIN

MWDTLTLPLRAGGSMSLNRDVLGVRNAGSDTMLIYVEPQYCLSKRALVERGDTPTYIANYRSLPGVGSRSRERLLRGRRRRRSWHWNTTPDFAFSPSHSLASLRRRRRTPLLSSFLLSSFLLSFFLLFFFLLNGVLGCCPHPQIGRWCSCDMAGQYPPLFSVPCLFDQLSLFPLLGCDSNFLIWGKIPISPYWVLKILLPKGKMKRGVDENNKGPMFPRLHVNDTEKGGPRAPPRNKMALYEQLSIPSQRLNGGQPINPN...

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_025916`
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_025916

Location Chr05:118535309-118541283 (+)

Description Similar to ELF3: Protein EARLY FLOWERING 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g25930`	May be a transcription factor part of a circadian clock input pathway.	ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway.2001 · DOI: 10.1105/tpc.13.6.1293 ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock.2012 · DOI: 10.4161/psb.18766 EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock.2012 · DOI: 10.1105/tpc.111.093807

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0142600`	Involved in the regulation of flowering time under short day (SD) and long day (LD) conditions.	Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering.2012 · DOI: 10.1093/pcp/pcs028 OsELF3-1, an ortholog of Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering.2012 · DOI: 10.1371/journal.pone.0043705
`Os01g0566100`	Involved in the regulation of flowering time.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025916 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006351 DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009409 response to cold Biological Process

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

GO:0009649 entrainment of circadian clock Biological Process

GO:0009733 response to auxin Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010031 circumnutation Biological Process

KEGG gene cross-reference

ath:AT2G25930

dosa:Os01g0566100

dosa:Os06g0142600

osa:4327931

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.

Nucleus0.906

Rank 1 · LXL04_025916 · OH-1004

Cytoplasm0.140

Rank 2 · LXL04_025916 · OH-1004

Cell membrane0.050

Rank 3 · LXL04_025916 · OH-1004

Endoplasmic reticulum0.036

Rank 4 · LXL04_025916 · OH-1004

Plastid0.017

Rank 5 · LXL04_025916 · 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.

PF27565.1ELF3_helical441-467 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025916	`PF27565.1`	ELF3_helical	441	467	6e-13	49.0

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
`O82804`	Arabidopsis thaliana	Protein EARLY FLOWERING 3	33.273%	Swiss-Prot	moderate database homology
`Q9SNQ6`	Oryza sativa subsp. japonica	Protein HEADING DATE 3B	32.524%	Swiss-Prot	weak database homology
`Q657D6`	Oryza sativa subsp. japonica	ELF3-like protein 2	33.081%	Swiss-Prot	weak database homology

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