LXL04_005626 | RubberDandelionOmics

Gene overview

LXL04_005626

Reference: OH-1004 Chr: Chr01 Coordinates: 169497445-169498440 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

996 bp · LXL04_005626|LXL04_005626|OH1004|cDNA

ATGGTAATCACTGGAAGAGAAACCTGTCCATGGGAGATGATGCTAGAAGATCCAAGGGCTTATGCTCTCTTGCCGTTCTCCGGCATCTCAATGAAAGACGATGGTCGTCACGACTCGGCCATGTTTGAAGAGTTAACTACGCTACCGCTACAGCTCCGCCACCTCCAAATGGCGGAATACGGCGACTCGTATGATGTTGCGGAGAAGGAAGGAGATGTAGAAATGGACGATTACTTCTGTATGTATGAGTTCAAGGTGAA...

CDS

Download CDS FASTA

996 bp · LXL04_005626|LXL04_005626|OH1004|CDS

ATGGTAATCACTGGAAGAGAAACCTGTCCATGGGAGATGATGCTAGAAGATCCAAGGGCTTATGCTCTCTTGCCGTTCTCCGGCATCTCAATGAAAGACGATGGTCGTCACGACTCGGCCATGTTTGAAGAGTTAACTACGCTACCGCTACAGCTCCGCCACCTCCAAATGGCGGAATACGGCGACTCGTATGATGTTGCGGAGAAGGAAGGAGATGTAGAAATGGACGATTACTTCTGTATGTATGAGTTCAAGGTGAA...

Protein

Download Protein FASTA

331 aa · LXL04_005626|LXL04_005626|OH1004|PROTEIN

MVITGRETCPWEMMLEDPRAYALLPFSGISMKDDGRHDSAMFEELTTLPLQLRHLQMAEYGDSYDVAEKEGDVEMDDYFCMYEFKVKRCARGRSHDWTDCPYTHSGEKARRRDPRKFHYSGNPCPEFRKGSCMKGDLCESAHGVFECWLHPSRYRTQPCKDGVHCSRRICFFAHTPEQLRILPPSQHHQVLIPHSNRTESYDGSPRRLATDFSPSTYFSSSSSPTSTLYFPHCSTPMDSPPMSPVSSLDLVSSMRNLQIG...

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_005626`
TK1151 ID	TkA01G029140
OH-1004 ID	LXL04_005626
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.000
Protein coverage (%)	TK1151 98.661 / OH-1004 70.393 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_005626

Location Chr01:169497445-169498440 (+)

Description Similar to Os01g0192000: 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
`At2g19810`	Zinc finger CCCH domain-containing protein 20.	No verified direct reference in this release
`At2g25900`	Zinc finger CCCH domain-containing protein 23.	No verified direct reference in this release
`At4g29190`	Zinc finger CCCH domain-containing protein 49.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0192000`	Involved in leaf senescence delay.	No verified direct reference in this release
`Os05g0195200`	Zinc finger CCCH domain-containing protein 35.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005626 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0010150 leaf senescence Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051607 defense response to virus Biological Process

GO:0061157 mRNA destabilization Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT2G19810

ath:AT2G25900

ath:AT4G29190

dosa:Os01g0192000

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.

Cytoplasm0.528

Rank 1 · LXL04_005626 · OH-1004

Nucleus0.507

Rank 2 · LXL04_005626 · OH-1004

Mitochondrion0.062

Rank 3 · LXL04_005626 · OH-1004

Cell membrane0.044

Rank 4 · LXL04_005626 · OH-1004

Endoplasmic reticulum0.026

Rank 5 · LXL04_005626 · 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_AtC3H2379-111 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005626	`PF25512.2`	zf-CCCH_AtC3H23	79	111	2e-19	69.7

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
`O82199`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 20	46.012%	Swiss-Prot	moderate database homology
`O82307`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 23	45.062%	Swiss-Prot	moderate database homology
`Q9M0G2`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 49	48.148%	Swiss-Prot	moderate database homology
`Q9FU27`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 2	44.737%	Swiss-Prot	moderate database homology
`Q6L4N4`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 35	46.580%	Swiss-Prot	moderate database homology

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