LXL04_017012 | RubberDandelionOmics

Gene overview

LXL04_017012

Reference: OH-1004 Chr: Chr03 Coordinates: 138845933-138848999 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1647 bp · LXL04_017012|LXL04_017012|OH1004|cDNA

ATGAAAAAGAAATCGAATAAAGCTTACAACAAGGTAGATTATGCAGAAGAATGGTGCTTTCAATGCAAAGATGGTGGCGATTTAATCATTTGCGACCACAAGAATTGTTTCAAGTCGTATCATTCACATCCAGAATGCACACAACAGGGCAAGTCATCTATAAATCGTCGATTTATATGTGTTCTGCATAAATGTGATGTTTGTGGTAGAGCTTCCGATGTCCATTGTTATGGCTGTCCGAAAGGTGTATGCAGACGCTG...

CDS

Download CDS FASTA

1638 bp · LXL04_017012|LXL04_017012|OH1004|CDS

ATGAAAAAGAAATCGAATAAAGCTTACAACAAGGTAGATTATGCAGAAGAATGGTGCTTTCAATGCAAAGATGGTGGCGATTTAATCATTTGCGACCACAAGAATTGTTTCAAGTCGTATCATTCACATCCAGAATGCACACAACAGGGCAAGTCATCTATAAATCGTCGATTTATATGTGTTCTGCATAAATGTGATGTTTGTGGTAGAGCTTCCGATGTCCATTGTTATGGCTGTCCGAAAGGTGTATGCAGACGCTG...

Protein

Download Protein FASTA

545 aa · LXL04_017012|LXL04_017012|OH1004|PROTEIN

MKKKSNKAYNKVDYAEEWCFQCKDGGDLIICDHKNCFKSYHSHPECTQQGKSSINRRFICVLHKCDVCGRASDVHCYGCPKGVCRRCIKSTDFVHVKGKKGFCSYCLKLSLLIEENKDVDSDGETIDFNNRDTYETLYKEYWEIINAKEKLTLDDLISANGQLNTGKNYDSDKYDDSDGYQCSDYEEKGDDDDMELHEKKPKKPKPESSKTKRKGQEKLKPKSKEKEKLKSNKEEFMGWGSTRLIKFLSYIEKDTTNPLS...

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_017012`
TK1151 ID	TkA02G084190
OH-1004 ID	LXL04_017012
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.400
Protein coverage (%)	TK1151 73.786 / OH-1004 97.615 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_017012

Location Chr03:138845933-138848999 (+)

Description Similar to At5g08430: Uncharacterized protein At5g08430

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g08430`	Uncharacterized protein At5g08430.	No verified direct reference in this release
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017012 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006302 double-strand break repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0032259 methylation Biological Process

GO:0070201 regulation of establishment of protein localization Biological Process

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

GO:2001032 regulation of double-strand break repair via nonhomologous end joining Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT2G16485

ath:AT5G08430

hsa:7468

mmu:107823

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.

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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.

Nucleus0.957

Rank 1 · LXL04_017012 · OH-1004

Cytoplasm0.121

Rank 2 · LXL04_017012 · OH-1004

Cell membrane0.017

Rank 3 · LXL04_017012 · OH-1004

Mitochondrion0.011

Rank 4 · LXL04_017012 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_017012 · 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.

PF03126.24Plus-3385-482 aa

PF25980.1NERD_plant504-534 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017012	`PF03126.24`	Plus-3	385	482	3.5e-14	53.9
LXL04_017012	`PF25980.1`	NERD_plant	504	534	5.3e-16	58.9

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
`Q9FT92`	Arabidopsis thaliana	Uncharacterized protein At5g08430	41.270%	Swiss-Prot	moderate database homology
`Q9SIV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 19	28.172%	Swiss-Prot	weak database homology
`Q9SD34`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 44	27.324%	Swiss-Prot	weak database homology

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