LXL04_021847 | RubberDandelionOmics

Gene overview

LXL04_021847

Reference: OH-1004 Chr: Chr04 Coordinates: 138563694-138565451 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1758 bp · LXL04_021847|LXL04_021847|OH1004|cDNA

ATGGAGGGAGTGGCGTTTCAAGAAAAGAAATTTAGGGTTCTATTGAAATGCTCGAATTTGCTCGAATTAGCAGCTGCAGATGATGTTTCTGGGTTCGTTTCAGAGGTAGAAGGAAAGAGGATCGATTTAGAAGAAGTTGGATTTTGGTACGGAAGAAGGAATTCATGTAAAGGAAAAATGGGATTTGAAGAACGAACTTCTCTCATGATTGCTTCGGTTTATGGAAGCATTCGAGTTTTGAAATACTTAATCGATAAAAA...

CDS

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1758 bp · LXL04_021847|LXL04_021847|OH1004|CDS

ATGGAGGGAGTGGCGTTTCAAGAAAAGAAATTTAGGGTTCTATTGAAATGCTCGAATTTGCTCGAATTAGCAGCTGCAGATGATGTTTCTGGGTTCGTTTCAGAGGTAGAAGGAAAGAGGATCGATTTAGAAGAAGTTGGATTTTGGTACGGAAGAAGGAATTCATGTAAAGGAAAAATGGGATTTGAAGAACGAACTTCTCTCATGATTGCTTCGGTTTATGGAAGCATTCGAGTTTTGAAATACTTAATCGATAAAAA...

Protein

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585 aa · LXL04_021847|LXL04_021847|OH1004|PROTEIN

MEGVAFQEKKFRVLLKCSNLLELAAADDVSGFVSEVEGKRIDLEEVGFWYGRRNSCKGKMGFEERTSLMIASVYGSIRVLKYLIDKNIDVNKTSGSDGVTALHCAAAGGSVASIEVVKMLLDAGADVNLTDGNGNKPGDLIARGIKSSIRKGLEMLLKGFVIEEIVAAKKEYPVDLSLPDINNAVYGSDEFRMYTFKVKPCSRAYTHDWTECPFVHPGENARRRDPKKFNYSCVPCPEFRKGSCVNGDACEYAHGVFESW...

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_021847`
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_021847

Location Chr04:138563694-138565451 (-)

Description Similar to At2g40140: Zinc finger CCCH domain-containing protein 29

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40140`	Involved in salt stress response.	No verified direct reference in this release
`At3g55980`	Involved in salt stress response.	No verified direct reference in this release
`At5g58620`	Zinc finger CCCH domain-containing protein 66.	No verified direct reference in this release
`At5g12850`	Zinc finger CCCH domain-containing protein 56.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0698800`	Zinc finger CCCH domain-containing protein 24.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021847 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006412 translation Biological Process

GO:0009409 response to cold Biological Process

GO:0009651 response to salt stress Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0080090 regulation of primary metabolic process Biological Process

GO:0000932 P-body Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT2G40140

ath:AT3G55980

ath:AT5G12850

ath:AT5G58620

dosa:Os03g0698800

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.

Cytoplasm0.553

Rank 1 · LXL04_021847 · OH-1004

Nucleus0.381

Rank 2 · LXL04_021847 · OH-1004

Cell membrane0.090

Rank 3 · LXL04_021847 · OH-1004

Golgi apparatus0.048

Rank 4 · LXL04_021847 · OH-1004

Mitochondrion0.046

Rank 5 · LXL04_021847 · 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.

PF12796.14Ank_259-131 aa

PF13637.13Ank_469-114 aa

PF00023.37Ank97-131 aa

PF25512.2zf-CCCH_AtC3H23190-223 aa

PF18044.8zf-CCCH_4235-254 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021847	`PF12796.14`	Ank_2	59	131	3.1e-12	47.6
LXL04_021847	`PF13637.13`	Ank_4	69	114	4e-13	49.9
LXL04_021847	`PF00023.37`	Ank	97	131	8.2e-13	48.5
LXL04_021847	`PF25512.2`	zf-CCCH_AtC3H23	190	223	1.8e-20	73.1
LXL04_021847	`PF18044.8`	zf-CCCH_4	235	254	5.1e-06	26.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9XEE6`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 29	50.242%	Swiss-Prot	strong database homology
`Q93ZS9`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 47	51.010%	Swiss-Prot	strong database homology
`Q9LUZ4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 66	46.190%	Swiss-Prot	moderate database homology
`Q9LXV4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 56	39.494%	Swiss-Prot	moderate database homology
`Q10EL1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 24	40.804%	Swiss-Prot	moderate database homology

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