LXL04_012591 | RubberDandelionOmics

Gene overview

LXL04_012591

Reference: OH-1004 Chr: Chr03 Coordinates: 15229259-15232098 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1407 bp · LXL04_012591|LXL04_012591|OH1004|cDNA

ATGGCGGGTAATGGCAGAGGAACCGCTGGAGATTATTTATCGGGGAAACGGACGCATGACGGAGACCGGAGGACAGTATATGGGAGTGACTATCGGTTCAGTTCTTGTAACGTGGAAGATAATCGCGCTTTTCGTAAGGATTACCATGGCCCAGATCTCGAAGCTAGGGCTGAACCAAAGACGCCTAACTTTCCTGGGTTTCCCAAAAATGAAGCGATGCATGAAGAGGAAGTAGAGAAGTTTGTTGAAGAGCATTATAA...

CDS

Download CDS FASTA

1407 bp · LXL04_012591|LXL04_012591|OH1004|CDS

ATGGCGGGTAATGGCAGAGGAACCGCTGGAGATTATTTATCGGGGAAACGGACGCATGACGGAGACCGGAGGACAGTATATGGGAGTGACTATCGGTTCAGTTCTTGTAACGTGGAAGATAATCGCGCTTTTCGTAAGGATTACCATGGCCCAGATCTCGAAGCTAGGGCTGAACCAAAGACGCCTAACTTTCCTGGGTTTCCCAAAAATGAAGCGATGCATGAAGAGGAAGTAGAGAAGTTTGTTGAAGAGCATTATAA...

Protein

Download Protein FASTA

468 aa · LXL04_012591|LXL04_012591|OH1004|PROTEIN

MAGNGRGTAGDYLSGKRTHDGDRRTVYGSDYRFSSCNVEDNRAFRKDYHGPDLEARAEPKTPNFPGFPKNEAMHEEEVEKFVEEHYKPFRSKYGGVSVGTWCRVKRGKYMGDLAQVVNVNEFQRKATVKLLPRIDLQAMVKKYSGVADYQYTSPAPRLITSGELNAYRLRVRQSLDPDTGDLYEVFDGMKLKDGYVFKKLALDSLNFSNFKPSEAELMKFNGKPDESNYVNNKQTMNNNNQVGEGLSSSYMNNNFEVPDR...

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_012591`
TK1151 ID	TkA02G551230
OH-1004 ID	LXL04_012591
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 97.356 / OH-1004 86.538 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_012591

Location Chr03:15229259-15232098 (+)

Description Similar to RDM3: Protein RNA-directed DNA methylation 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g04290`	Effector of RNA-directed DNA methylation (RdDM) triggered by small interfering RNAs (siRNAs, 24-nt RNAs).	An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein.2009 · DOI: 10.1016/j.cell.2009.04.028 Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242 Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing.2011 · DOI: 10.1371/journal.pgen.1002120
`At2g34210`	May regulate transcription elongation by RNA polymerase II.	No verified direct reference in this release
`At4g08350`	May regulate transcription elongation by RNA polymerase II.	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_012591 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006412 translation Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0032784 regulation of DNA-templated transcription elongation 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:0005840 ribosome Cellular Component

KEGG gene cross-reference

ath:AT2G34210

ath:AT4G08350

ath:AT5G04290

cne:CNA06210

uma:UMAG_10033

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.

Nucleus0.808

Rank 1 · LXL04_012591 · OH-1004

Cytoplasm0.193

Rank 2 · LXL04_012591 · OH-1004

Cell membrane0.048

Rank 3 · LXL04_012591 · OH-1004

Endoplasmic reticulum0.030

Rank 4 · LXL04_012591 · OH-1004

Plastid0.029

Rank 5 · LXL04_012591 · 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.

PF23042.3KOW1_SPT597-220 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012591	`PF23042.3`	KOW1_SPT5	97	220	4.1e-23	83.1

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
`F4JW79`	Arabidopsis thaliana	Protein RNA-directed DNA methylation 3	50.000%	Swiss-Prot	weak database homology
`O80770`	Arabidopsis thaliana	Putative transcription elongation factor SPT5 homolog 2	37.342%	Swiss-Prot	weak database homology
`Q9STN3`	Arabidopsis thaliana	Putative transcription elongation factor SPT5 homolog 1	42.446%	Swiss-Prot	weak database homology

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