LXL04_003943 | RubberDandelionOmics

Gene overview

LXL04_003943

Reference: OH-1004 Chr: Chr01 Coordinates: 116817136-116818256 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

867 bp · LXL04_003943|LXL04_003943|OH1004|cDNA

ATGTCGGTAATCTTTGAAGATGAAATAACCGAAAACAATCTGGACTTCTACCAGTTTGGCCTTCATCATGACCAGTTTGATCTATCTCTAATCCAAAACCAAATCCCACTAACAGATCACATCGATGCCTTCAATTGCCAGATTCCGGCGTATCCTCATACTCATCCAAACGATCATGTTGTCCCAATACTGGGACCCACATTGCCCATGATCTGTGAAGATGACTGCCTATCTTCCATGCCACCTTCAAAGTTTATGCG...

CDS

Download CDS FASTA

867 bp · LXL04_003943|LXL04_003943|OH1004|CDS

ATGTCGGTAATCTTTGAAGATGAAATAACCGAAAACAATCTGGACTTCTACCAGTTTGGCCTTCATCATGACCAGTTTGATCTATCTCTAATCCAAAACCAAATCCCACTAACAGATCACATCGATGCCTTCAATTGCCAGATTCCGGCGTATCCTCATACTCATCCAAACGATCATGTTGTCCCAATACTGGGACCCACATTGCCCATGATCTGTGAAGATGACTGCCTATCTTCCATGCCACCTTCAAAGTTTATGCG...

Protein

Download Protein FASTA

288 aa · LXL04_003943|LXL04_003943|OH1004|PROTEIN

MSVIFEDEITENNLDFYQFGLHHDQFDLSLIQNQIPLTDHIDAFNCQIPAYPHTHPNDHVVPILGPTLPMICEDDCLSSMPPSKFMRLNKITSSPNCLFMDAEVISYLSGNSNHPLSVESSGNFNGNMFLGNEIQPLELDYKGVNGSIFCPDPLHRPCNPNELQASEITNLEADTLRVTSKLTTEERKEKIHRYMKKRTERNFSKKIKYACRKTLADSRPRVRGRFAKNDEYGENNRRTWSNHEEDSTDEEKYFQVLVKE...

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_003943`
TK1151 ID	TkA01G226280
OH-1004 ID	LXL04_003943
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_003943

Location Chr01:116817136-116818256 (-)

Description Similar to COL4: Zinc finger protein CONSTANS-LIKE 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g24930`	Zinc finger protein CONSTANS-LIKE 4.	No verified direct reference in this release
`At2g24790`	Zinc finger protein CONSTANS-LIKE 3.	No verified direct reference in this release
`At3g02380`	Putative transcription factor.	No verified direct reference in this release
`At5g57180`	Responsible for specific up-regulation of the translocon genes TOC33 and TOC75 in leaves.	CIA2 coordinately up-regulates protein import and synthesis in leaf chloroplasts.2009 · DOI: 10.1104/pp.109.137240

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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003943 · 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:0009658 chloroplast organization Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010099 regulation of photomorphogenesis Biological Process

GO:0010161 red light signaling pathway Biological Process

GO:0032922 circadian regulation of gene expression Biological Process

GO:0045036 protein targeting to chloroplast Biological Process

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

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G24790

ath:AT3G02380

ath:AT5G24930

ath:AT5G57180

dosa:Os09g0240200

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.

Nucleus0.884

Rank 1 · LXL04_003943 · OH-1004

Cytoplasm0.250

Rank 2 · LXL04_003943 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_003943 · OH-1004

Mitochondrion0.019

Rank 4 · LXL04_003943 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_003943 · 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.

PF06203.20CCT187-229 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003943	`PF06203.20`	CCT	187	229	6.5e-19	68.4

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
`Q940T9`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 4	49.091%	Swiss-Prot	weak database homology
`Q9SK53`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 3	42.254%	Swiss-Prot	weak database homology
`Q96502`	Arabidopsis thaliana	Zinc finger protein CONSTANS-LIKE 2	44.262%	Swiss-Prot	weak database homology
`Q9LU68`	Arabidopsis thaliana	Protein CHLOROPLAST IMPORT APPARATUS 2	38.043%	Swiss-Prot	weak database homology
`O82117`	Oryza sativa subsp. japonica	Zinc finger protein CO3	50.000%	Swiss-Prot	weak database homology

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