LXL04_019936 | RubberDandelionOmics

Gene overview

LXL04_019936

Reference: OH-1004 Chr: Chr04 Coordinates: 44729281-44730528 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1092 bp · LXL04_019936|LXL04_019936|OH1004|cDNA

ATGGATGGTGTTTATCCAGAACAAGAACACAGTAAGTTTCTGTACCTTGCAAGCAAGAAATCCTTCCGGGACCTCGACATCCCACCTCGCAAGCTTCTCAGTCGCCGACTTGCATCTCTATCACCGGAACAATCCATGGAATTGTACCATCAGCTCCAGCAACAACAAAATGACTCCCCTAGGGTCCTCCCAGAAGAAACACTGCTACAGAAATTCCTCCCTTACAATTCCGGTCACGACAATGACTCCGATCCCTACGC...

CDS

Download CDS FASTA

1092 bp · LXL04_019936|LXL04_019936|OH1004|CDS

ATGGATGGTGTTTATCCAGAACAAGAACACAGTAAGTTTCTGTACCTTGCAAGCAAGAAATCCTTCCGGGACCTCGACATCCCACCTCGCAAGCTTCTCAGTCGCCGACTTGCATCTCTATCACCGGAACAATCCATGGAATTGTACCATCAGCTCCAGCAACAACAAAATGACTCCCCTAGGGTCCTCCCAGAAGAAACACTGCTACAGAAATTCCTCCCTTACAATTCCGGTCACGACAATGACTCCGATCCCTACGC...

Protein

Download Protein FASTA

363 aa · LXL04_019936|LXL04_019936|OH1004|PROTEIN

MDGVYPEQEHSKFLYLASKKSFRDLDIPPRKLLSRRLASLSPEQSMELYHQLQQQQNDSPRVLPEETLLQKFLPYNSGHDNDSDPYASDEFRMYEFKIRKCTRSRSHDWTDCPFAHPGEKARRRCPRRYNYSGNVCADFRRGSCSRGDACEFAHGVFECWLHPFRYRTEACKDGKNCQRKICFFAHTPKQLRSMPVESVISPGKHLNSGHCSSCRCHPGIHHANSPTSILDIDKLSPPTSPPFSTAPTGSGFSPVSRFSD...

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_019936`
TK1151 ID	TkA05G107280
OH-1004 ID	LXL04_019936
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.400
Protein coverage (%)	TK1151 93.732 / OH-1004 95.041 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_019936

Location Chr04:44729281-44730528 (+)

Description Similar to TZF4: Zinc finger CCCH domain-containing protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g03790`	Probable transcription repressor that functions as a negative regulator of phytochrome-mediated promotion of seed germination.	No verified direct reference in this release
`At5g44260`	Zinc finger CCCH domain-containing protein 61.	No verified direct reference in this release
`At4g29190`	Zinc finger CCCH domain-containing protein 49.	No verified direct reference in this release
`At2g19810`	Zinc finger CCCH domain-containing protein 20.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0195200`	Zinc finger CCCH domain-containing protein 35.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_019936 · 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:0006979 response to oxidative stress Biological Process

GO:0010187 negative regulation of seed germination Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051607 defense response to virus Biological Process

GO:0000932 P-body Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G03790

ath:AT2G19810

ath:AT4G29190

ath:AT5G44260

dosa:Os05g0195200

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.

Cytoplasm0.564

Rank 1 · LXL04_019936 · OH-1004

Nucleus0.412

Rank 2 · LXL04_019936 · OH-1004

Mitochondrion0.073

Rank 3 · LXL04_019936 · OH-1004

Cell membrane0.051

Rank 4 · LXL04_019936 · OH-1004

Endoplasmic reticulum0.030

Rank 5 · LXL04_019936 · 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.

PF25512.2zf-CCCH_AtC3H2390-123 aa

PF00642.31zf-CCCH135-155 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019936	`PF25512.2`	zf-CCCH_AtC3H23	90	123	1.5e-20	73.3
LXL04_019936	`PF00642.31`	zf-CCCH	135	155	6.8e-07	29.8

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
`Q9ZWA1`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 2	67.722%	Swiss-Prot	weak database homology
`Q9FKW2`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 61	60.465%	Swiss-Prot	weak database homology
`Q9M0G2`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 49	50.802%	Swiss-Prot	weak database homology
`O82199`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 20	62.143%	Swiss-Prot	weak database homology
`Q6L4N4`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 35	77.273%	Swiss-Prot	weak database homology

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