LXL04_013804 | RubberDandelionOmics

Gene overview

LXL04_013804

Reference: OH-1004 Chr: Chr03 Coordinates: 36155828-36162078 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4635 bp · LXL04_013804|LXL04_013804|OH1004|cDNA

ATGATGGAAGTTCAAAATTCCGGAGCTCAGAGTCAACCGATTCAGAAAACCGACGCCGATGGGACGAGGTTGGTCGGAGGGCAAGTGGGAGTCGTTGCAGATGGTGGCGGTGGAGGAGTGAAGGTTGAGGTAGGTAATGTCGTTGAAGTGGCGAAGAGGAAGCGAGGGCGGCCGCCTAAGTCTCAGGCGAACCAGCCGTCTGCTAAGAAAATTAAAGAAGAGGACGAGGACGAAGACGTTTGTTTTATTTGCTTTGATGG...

CDS

Download CDS FASTA

4635 bp · LXL04_013804|LXL04_013804|OH1004|CDS

ATGATGGAAGTTCAAAATTCCGGAGCTCAGAGTCAACCGATTCAGAAAACCGACGCCGATGGGACGAGGTTGGTCGGAGGGCAAGTGGGAGTCGTTGCAGATGGTGGCGGTGGAGGAGTGAAGGTTGAGGTAGGTAATGTCGTTGAAGTGGCGAAGAGGAAGCGAGGGCGGCCGCCTAAGTCTCAGGCGAACCAGCCGTCTGCTAAGAAAATTAAAGAAGAGGACGAGGACGAAGACGTTTGTTTTATTTGCTTTGATGG...

Protein

Download Protein FASTA

1544 aa · LXL04_013804|LXL04_013804|OH1004|PROTEIN

MMEVQNSGAQSQPIQKTDADGTRLVGGQVGVVADGGGGGVKVEVGNVVEVAKRKRGRPPKSQANQPSAKKIKEEDEDEDVCFICFDGGSLVLCDRRGCPKAYHPACIKRDEAFFQTKAKWNCGWHICSMCEKTSHHMCYTCTYSLCKGCSKKADFMCVRGDKGFCTVCMKMITLIEHSAQGKEVKVDFDDKSSWEYLFKVYWLYTKGKLSLTFDEITQAQNPWKRSDTIASIPPPVHINTTGRRSITSELSNLEANERKL...

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_013804`
TK1151 ID	TkA02G471030
OH-1004 ID	LXL04_013804
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.300
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

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Basic Information and Functional Annotation

Gene ID LXL04_013804

Location Chr03:36155828-36162078 (-)

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_013804 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

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

GO:0005634 nucleus 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

GO:0042393 histone binding Molecular Function

GO:1990269 RNA polymerase II C-terminal domain phosphoserine binding Molecular Function

KEGG gene cross-reference

ath:AT2G16485

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.

Nucleus0.904

Rank 1 · LXL04_013804 · OH-1004

Cytoplasm0.136

Rank 2 · LXL04_013804 · OH-1004

Cell membrane0.058

Rank 3 · LXL04_013804 · OH-1004

Endoplasmic reticulum0.029

Rank 4 · LXL04_013804 · OH-1004

Plastid0.015

Rank 5 · LXL04_013804 · 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.

PF02201.24SWIB299-357 aa

PF03126.24Plus-3424-527 aa

PF25980.1NERD_plant552-612 aa

PF02213.22GYF911-949 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013804	`PF02201.24`	SWIB	299	357	6.2e-14	52.2
LXL04_013804	`PF03126.24`	Plus-3	424	527	2.3e-22	80.3
LXL04_013804	`PF25980.1`	NERD_plant	552	612	8.3e-16	58.2
LXL04_013804	`PF02213.22`	GYF	911	949	1.3e-13	51.2

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	50.927%	Swiss-Prot	weak database homology
`Q9SD34`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 44	49.921%	Swiss-Prot	weak database homology
`Q9FT92`	Arabidopsis thaliana	Uncharacterized protein At5g08430	29.532%	Swiss-Prot	weak database homology

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