LXL04_011830 | RubberDandelionOmics

Gene overview

LXL04_011830

Reference: OH-1004 Chr: Chr03 Coordinates: 1142287-1144709 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

930 bp · LXL04_011830|LXL04_011830|OH1004|cDNA

ATGTATGCTGAGACTGGCCTAATGTTTCCCTATTTTCAGAACTTCTCAACTGATGGTCAACAATTTGATGATTTCTGTCACTCACAGAAGTCTATTACTTGCTTGGTAATTCCATTTCTGGTCATCTTTGTCTGTCTTCAAGCTTTCTCTGCTAAATCTGCTCTTCCTTCCGTGATCTTGAATGCTGATAACCTAATTCAGACGTCCACTGTATCAGATTACGATCTTGGGGGAGAAGGGGATCTTTTCAAAGCACCCGA...

CDS

Download CDS FASTA

930 bp · LXL04_011830|LXL04_011830|OH1004|CDS

ATGTATGCTGAGACTGGCCTAATGTTTCCCTATTTTCAGAACTTCTCAACTGATGGTCAACAATTTGATGATTTCTGTCACTCACAGAAGTCTATTACTTGCTTGGTAATTCCATTTCTGGTCATCTTTGTCTGTCTTCAAGCTTTCTCTGCTAAATCTGCTCTTCCTTCCGTGATCTTGAATGCTGATAACCTAATTCAGACGTCCACTGTATCAGATTACGATCTTGGGGGAGAAGGGGATCTTTTCAAAGCACCCGA...

Protein

Download Protein FASTA

309 aa · LXL04_011830|LXL04_011830|OH1004|PROTEIN

MYAETGLMFPYFQNFSTDGQQFDDFCHSQKSITCLVIPFLVIFVCLQAFSAKSALPSVILNADNLIQTSTVSDYDLGGEGDLFKAPEPIIIEPLISGLDPITSTISMIACGEDTLSPQELKVTDIESLQKEEFLNDVFYECKNILAQEAAAATESSPLSEVLSFSFPVTTDENTENLHPSCQIPKSMSSDSLNSMDWIQGAQIKSSFLNFSELDFGNAYGMRRAFSDGDIKTLVDGNTGLIHYPLGQPPVMSERTLEDRM...

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_011830`
TK1151 ID	TkA02G609710
OH-1004 ID	LXL04_011830
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	90.900
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011830

Location Chr03:1142287-1144709 (+)

Description Similar to COL5: Zinc finger protein CONSTANS-LIKE 5

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g57660`	Zinc finger protein CONSTANS-LIKE 5.	No verified direct reference in this release
`At5g15850`	Putative transcription factor that may be involved in the light input to the circadian clock but does not affect flowering time.	No verified direct reference in this release
`At5g24930`	Zinc finger protein CONSTANS-LIKE 4.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0240200`	Probable transcription factor involved in the regulation of flowering time under short day (SD) conditions.	No verified direct reference in this release
`Os07g0261200`	Probable transcription factor involved in the regulation of flowering time under long day (LD) conditions.	Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.2008 · DOI: 10.1038/ng.143 Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response.2013 · DOI: 10.1111/tpj.12268

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011830 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0032922 circadian regulation of gene expression Biological Process

GO:0048577 negative regulation of short-day photoperiodism, flowering Biological Process

GO:0048579 negative regulation of long-day photoperiodism, flowering Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

ath:AT5G15850

ath:AT5G24930

ath:AT5G57660

dosa:Os09g0240200

osa:107276161

osa:4346474

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.

Nucleus0.597

Rank 1 · LXL04_011830 · OH-1004

Cytoplasm0.420

Rank 2 · LXL04_011830 · OH-1004

Cell membrane0.068

Rank 3 · LXL04_011830 · OH-1004

Mitochondrion0.052

Rank 4 · LXL04_011830 · OH-1004

Endoplasmic reticulum0.051

Rank 5 · LXL04_011830 · 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.

PF06203.20CCT259-301 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011830	`PF06203.20`	CCT	259	301	4.7e-17	62.5

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
`Q9FHH8`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 5	54.167%	Swiss-Prot	weak database homology
`O50055`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 1	50.000%	Swiss-Prot	weak database homology
`Q940T9`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 4	40.000%	Swiss-Prot	weak database homology
`O82117`	Oryza sativa subsp. japonica	Zinc finger protein CO3	36.047%	Swiss-Prot	weak database homology
`E5RQA1`	Oryza sativa subsp. japonica	Transcription factor GHD7	45.283%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card