LXL04_008559 | RubberDandelionOmics

Gene overview

LXL04_008559

Reference: OH-1004 Chr: Chr02 Coordinates: 102777085-102777908 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

621 bp · LXL04_008559|LXL04_008559|OH1004|cDNA

ATGTTTCAGAATGAAAATCAATTTCCCAAAAGACCAAGAATATCTGAACAGATGGCGAATCGAAGAACTCAATACAAAAGTGATCTGTGTTTGAGATTTCAAAGGGGTACTTGCGATTACGGTGATCGCTGTTGCTTCGCCCACGGCTATGGAGATCTCAGAGGACAGATTGCGCTTGATGAGGCTTCCCGTGTCAAATATATGGATGAAAACCAAAACCCTAGGTGTAGCGATAAATCGAGATTATGCTGGAGGTTCAT...

CDS

Download CDS FASTA

621 bp · LXL04_008559|LXL04_008559|OH1004|CDS

ATGTTTCAGAATGAAAATCAATTTCCCAAAAGACCAAGAATATCTGAACAGATGGCGAATCGAAGAACTCAATACAAAAGTGATCTGTGTTTGAGATTTCAAAGGGGTACTTGCGATTACGGTGATCGCTGTTGCTTCGCCCACGGCTATGGAGATCTCAGAGGACAGATTGCGCTTGATGAGGCTTCCCGTGTCAAATATATGGATGAAAACCAAAACCCTAGGTGTAGCGATAAATCGAGATTATGCTGGAGGTTCAT...

Protein

Download Protein FASTA

206 aa · LXL04_008559|LXL04_008559|OH1004|PROTEIN

MFQNENQFPKRPRISEQMANRRTQYKSDLCLRFQRGTCDYGDRCCFAHGYGDLRGQIALDEASRVKYMDENQNPRCSDKSRLCWRFMNGEKCQFGDKCHFYHIKTERKSDVISVLDVAGSGGMQQHKQTPWRTKLCNRWMSTGSCPYGLKCCFAHGESELLNQRSNGDGTFEKKIDGNRWEFKWKNVEKIGRVYADWINVTPAALA

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_008559`
TK1151 ID	TkA03G358800
OH-1004 ID	LXL04_008559
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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_008559

Location Chr02:102777085-102777908 (+)

Description Similar to At3g19360: Zinc finger CCCH domain-containing protein 39

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19360`	Zinc finger CCCH domain-containing protein 39.	No verified direct reference in this release
`At1g32360`	Zinc finger CCCH domain-containing protein 12.	No verified direct reference in this release
`At2g35430`	Zinc finger CCCH domain-containing protein 28.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0159800`	Zinc finger CCCH domain-containing protein 56.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008559 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000165 MAPK cascade Biological Process

GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0009611 response to wounding Biological Process

GO:0010837 regulation of keratinocyte proliferation Biological Process

GO:0031086 nuclear-transcribed mRNA catabolic process, deadenylation-independent decay Biological Process

GO:0032680 regulation of tumor necrosis factor production Biological Process

GO:0032703 negative regulation of interleukin-2 production Biological Process

GO:0032897 negative regulation of viral transcription Biological Process

KEGG gene cross-reference

ath:AT1G32360

ath:AT2G35430

ath:AT3G19360

dosa:Os08g0159800

hsa:7538

osa:4344715

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.

Nucleus0.813

Rank 1 · LXL04_008559 · OH-1004

Cytoplasm0.207

Rank 2 · LXL04_008559 · OH-1004

Mitochondrion0.034

Rank 3 · LXL04_008559 · OH-1004

Plastid0.031

Rank 4 · LXL04_008559 · OH-1004

Cell membrane0.030

Rank 5 · LXL04_008559 · 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.

PF00642.31zf-CCCH25-49 aa

PF00642.31zf-CCCH79-102 aa

PF18044.8zf-CCCH_481-102 aa

PF00642.31zf-CCCH131-157 aa

PF25585.2zf-CCCH_DUS3L133-155 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008559	`PF00642.31`	zf-CCCH	25	49	2.2e-23	82.3
LXL04_008559	`PF00642.31`	zf-CCCH	79	102	2.2e-23	82.3
LXL04_008559	`PF18044.8`	zf-CCCH_4	81	102	4.6e-12	46.1
LXL04_008559	`PF00642.31`	zf-CCCH	131	157	2.2e-23	82.3
LXL04_008559	`PF25585.2`	zf-CCCH_DUS3L	133	155	2.1e-10	41.1

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
`Q9LT81`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 39	25.081%	Swiss-Prot	weak database homology
`Q9LQM3`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 12	24.138%	Swiss-Prot	weak database homology
`Q5PP65`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 28	27.119%	Swiss-Prot	weak database homology
`Q84UQ3`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 56	28.421%	Swiss-Prot	weak database homology

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