LXL04_025397 | RubberDandelionOmics

Gene overview

LXL04_025397

Reference: OH-1004 Chr: Chr05 Coordinates: 111047417-111052591 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3588 bp · LXL04_025397|LXL04_025397|OH1004|cDNA

ATGGAGGTTGAAGATGTAAACGCCTCAAATCATCTTCAAGAATCGACAACAGCCGTATCAAATGAAAGCTTGTCAGAAAATAAAAGCATGAATGATATAGAATTAAAAGTAGAGGTACCGGAATCGAACACACAAGAAGAACAAGGAGAAAAATCGTCTGTTTTATCCCCTAAATTGGACGATCCAAATCATTTTGACCCGGGTGCAGAGGGGGGAACAGCTGAGGAGAAGGAGGTCATTGTCGAATGCCGGAACTCAGA...

CDS

Download CDS FASTA

3588 bp · LXL04_025397|LXL04_025397|OH1004|CDS

ATGGAGGTTGAAGATGTAAACGCCTCAAATCATCTTCAAGAATCGACAACAGCCGTATCAAATGAAAGCTTGTCAGAAAATAAAAGCATGAATGATATAGAATTAAAAGTAGAGGTACCGGAATCGAACACACAAGAAGAACAAGGAGAAAAATCGTCTGTTTTATCCCCTAAATTGGACGATCCAAATCATTTTGACCCGGGTGCAGAGGGGGGAACAGCTGAGGAGAAGGAGGTCATTGTCGAATGCCGGAACTCAGA...

Protein

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1195 aa · LXL04_025397|LXL04_025397|OH1004|PROTEIN

MEVEDVNASNHLQESTTAVSNESLSENKSMNDIELKVEVPESNTQEEQGEKSSVLSPKLDDPNHFDPGAEGGTAEEKEVIVECRNSEQTGGCWNSLVVEPTSLLKDEKDRAEDVISTSDVAATERGGSELPNSIKADVGECSAAVSVPDNGLDVVEETVNNREEETNTNVSFVNEDDKDGGAAVPLLPVAEIDEIEEVKEDVKSDGVEFVAGAELITEGEADVQVLAAEVVADEEEKAAGVTENDDEEPTVADEEKSVDT...

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_025397`
TK1151 ID	TkA06G061780
OH-1004 ID	LXL04_025397
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.800
Protein coverage (%)	TK1151 98.168 / OH-1004 67.280 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_025397

Location Chr05:111047417-111052591 (+)

Description Similar to NERD: Zinc finger CCCH domain-containing protein 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q9SIV5`	Plays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences.	No verified direct reference in this release
`At3g51120`	Zinc finger CCCH domain-containing protein 44.	No verified direct reference in this release
`At5g08430`	Uncharacterized protein At5g08430.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025397 · 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:0032259 methylation Biological Process

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

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016593 Cdc73/Paf1 complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G16485

ath:AT5G08430

hsa:54904

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.

Nucleus0.952

Rank 1 · LXL04_025397 · OH-1004

Cytoplasm0.112

Rank 2 · LXL04_025397 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_025397 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_025397 · OH-1004

Mitochondrion0.009

Rank 5 · LXL04_025397 · 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.

PF02201.24SWIB524-597 aa

PF03126.24Plus-3657-754 aa

PF25980.1NERD_plant777-816 aa

PF02213.22GYF933-973 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025397	`PF02201.24`	SWIB	524	597	9.8e-14	51.6
LXL04_025397	`PF03126.24`	Plus-3	657	754	7.3e-20	72.2
LXL04_025397	`PF25980.1`	NERD_plant	777	816	5.9e-09	36.3
LXL04_025397	`PF02213.22`	GYF	933	973	4e-14	52.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SIV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 19	38.760%	Swiss-Prot	moderate database homology
`Q9SD34`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 44	45.580%	Swiss-Prot	moderate database homology
`Q9FT92`	Arabidopsis thaliana	Uncharacterized protein At5g08430	31.856%	Swiss-Prot	weak database homology

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