LXL04_028860 | RubberDandelionOmics

Gene overview

LXL04_028860

Reference: OH-1004 Chr: Chr06 Coordinates: 71389257-71394379 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3663 bp · LXL04_028860|LXL04_028860|OH1004|cDNA

ATGGAAGAGACTGAGCTTGAAGAAGGAGAGGCTTGTTTTGACGACAATGACGCATGCATTGACCCTGATACAGCTCTCTCTTACATTGATGAGAGGCTGCAAAATGTATTGGGACATTTTCAGAAATATTTTGAAGGTGAAGGGTGTGCAGAAATGTTGGGTCCAATATTTGGTGGGTATGGGTCTTTCTTACCCGTACATAAGCAACTTCCAACTCTGCATTCCCATATCAAGACCCCTCAAACAGTTCAGATTCCCAA...

CDS

Download CDS FASTA

3663 bp · LXL04_028860|LXL04_028860|OH1004|CDS

ATGGAAGAGACTGAGCTTGAAGAAGGAGAGGCTTGTTTTGACGACAATGACGCATGCATTGACCCTGATACAGCTCTCTCTTACATTGATGAGAGGCTGCAAAATGTATTGGGACATTTTCAGAAATATTTTGAAGGTGAAGGGTGTGCAGAAATGTTGGGTCCAATATTTGGTGGGTATGGGTCTTTCTTACCCGTACATAAGCAACTTCCAACTCTGCATTCCCATATCAAGACCCCTCAAACAGTTCAGATTCCCAA...

Protein

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1220 aa · LXL04_028860|LXL04_028860|OH1004|PROTEIN

MEETELEEGEACFDDNDACIDPDTALSYIDERLQNVLGHFQKYFEGEGCAEMLGPIFGGYGSFLPVHKQLPTLHSHIKTPQTVQIPNKSCLQGPPLNSTRPPANSSSHVSKNETTTSNPRSLKVRIKVGCDKSARKNAAIYSGLGLSSPSSSMGNDHEDSDGIPLDSPATILHNMTSILVPGNRLLSPLNESLLCLPKMERIIENKPKPPIMGRKFGIVDDSSCILMNGNEVSSQEKSEMEGTKCKESRSVPLSRKDLKV...

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_028860`
TK1151 ID	TkA07G241780
OH-1004 ID	LXL04_028860
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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_028860

Location Chr06:71389257-71394379 (-)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g32010`	Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3.	Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.2007 · DOI: 10.1104/pp.106.092320

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0347300`	Binds to histones H3K4me1, H3K4me2 and H3K4me3 in GST pull-down assay.	No verified direct reference in this release
`Os07g0669800`	Transcriptional activator that acts as a positive regulator of grain size.	No verified direct reference in this release
`Os05g0371100`	Binds to histones H3K4me1, H3K4me2 and H3K4me3 in GST pull-down assay.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028860 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0080113 regulation of seed growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

dosa:Os03g0347300

dosa:Os07g0669800

osa:4344236

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.

Nucleus0.971

Rank 1 · LXL04_028860 · OH-1004

Cytoplasm0.077

Rank 2 · LXL04_028860 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_028860 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_028860 · OH-1004

Plastid0.009

Rank 5 · LXL04_028860 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF07496.22zf-CW444-490 aa

PF24756.2THD_CWZF3-5-7975-1207 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028860	`PF07496.22`	zf-CW	444	490	1.9e-16	60.5
LXL04_028860	`PF24756.2`	THD_CWZF3-5-7	975	1207	5.8e-50	171.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q5CCK4`	Arabidopsis thaliana	B3 domain-containing transcription repressor VAL2	34.862%	Swiss-Prot	weak database homology
`Q0DRX6`	Oryza sativa subsp. japonica	Cysteine-tryptophan domain-containing zinc finger protein 3	35.662%	Swiss-Prot	weak database homology
`A0A0P0X9Z7`	Oryza sativa subsp. japonica	Cysteine-tryptophan domain-containing zinc finger protein 7	41.841%	Swiss-Prot	weak database homology
`Q0DIQ5`	Oryza sativa subsp. japonica	Cysteine-tryptophan domain-containing zinc finger protein 5	34.363%	Swiss-Prot	weak database homology

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