LXL04_034820 | RubberDandelionOmics

Gene overview

LXL04_034820

Reference: OH-1004 Chr: Chr08 Coordinates: 3339679-3344212 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3654 bp · LXL04_034820|LXL04_034820|OH1004|cDNA

ATGGAAGACGCAGGACCAAGCTCCAAGGAGAAGCCGTCAAATGGATCTGTACATGTCGACAtagatgaagaagatgatgatgatgatatgATGGACGCACCATCAGTTAGGGATTTCGATGAGTCCTTCTTAAAGAGCTTCTGTAGAAGGGCATCCTCGTCCTTTTTCAAACACTATGGTCTTATAAGTCATCAGATCAACTCATATGACGACTTCATCAAAGTAGGAATCCAGAATGTTTTCGACTCCATTGGTGAGAT...

CDS

Download CDS FASTA

3654 bp · LXL04_034820|LXL04_034820|OH1004|CDS

ATGGAAGACGCAGGACCAAGCTCCAAGGAGAAGCCGTCAAATGGATCTGTACATGTCGACATAGATGAAGAAGATGATGATGATGATATGATGGACGCACCATCAGTTAGGGATTTCGATGAGTCCTTCTTAAAGAGCTTCTGTAGAAGGGCATCCTCGTCCTTTTTCAAACACTATGGTCTTATAAGTCATCAGATCAACTCATATGACGACTTCATCAAAGTAGGAATCCAGAATGTTTTCGACTCCATTGGTGAGAT...

Protein

Download Protein FASTA

1217 aa · LXL04_034820|LXL04_034820|OH1004|PROTEIN

MEDAGPSSKEKPSNGSVHVDIDEEDDDDDMMDAPSVRDFDESFLKSFCRRASSSFFKHYGLISHQINSYDDFIKVGIQNVFDSIGEIIVEPGYDPSKKGENEWRYASIKFGKVTLERPRFYTGDKSESGNKFLDFLPRHARLQNMTYSSRMKVQFTKEVTTIIAFSYIFSPITYHMKFQVYIQELVRSDKFKTGKEKYIDKKILETEEREVYIGRIPVMVNSDTCWMSGPDRKDDCDYDQGGYFIIKGAEKTFIAQEQLG...

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_034820`
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_034820

Location Chr08:3339679-3344212 (-)

Description Similar to NRPD2: DNA-directed RNA polymerases IV and V subunit 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g23780`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Atypical RNA polymerase subunits required for RNA-directed DNA methylation.2005 · DOI: 10.1038/ng1580 Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.2005 · DOI: 10.1101/gad.348405 Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing.2010 · DOI: 10.1111/j.1365-313x.2010.04358.x
`At3g18090`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	No verified direct reference in this release
`At4g21710`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	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_034820 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006354 DNA-templated transcription elongation Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing Biological Process

GO:0035196 miRNA processing Biological Process

GO:0050776 regulation of immune response Biological Process

GO:0050832 defense response to fungus Biological Process

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

GO:0141007 transposable element silencing by siRNA-mediated heterochromatin formation Biological Process

KEGG gene cross-reference

ath:AT3G18090

ath:AT3G23780

ath:AT4G21710

ddi:DDB_G0288257

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.

Nucleus0.953

Rank 1 · LXL04_034820 · OH-1004

Cytoplasm0.067

Rank 2 · LXL04_034820 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_034820 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_034820 · OH-1004

Plastid0.011

Rank 5 · LXL04_034820 · 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.

PF04563.21RNA_pol_Rpb2_160-478 aa

PF04561.20RNA_pol_Rpb2_2313-444 aa

PF04565.22RNA_pol_Rpb2_3520-581 aa

PF04566.19RNA_pol_Rpb2_4617-678 aa

PF04567.23RNA_pol_Rpb2_5693-736 aa

PF00562.34RNA_pol_Rpb2_6745-1114 aa

PF04560.26RNA_pol_Rpb2_71116-1213 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_034820	`PF04563.21`	RNA_pol_Rpb2_1	60	478	1.2e-32	113.8
LXL04_034820	`PF04561.20`	RNA_pol_Rpb2_2	313	444	3.3e-11	43.9
LXL04_034820	`PF04565.22`	RNA_pol_Rpb2_3	520	581	8e-15	55.5
LXL04_034820	`PF04566.19`	RNA_pol_Rpb2_4	617	678	8.4e-21	74.5
LXL04_034820	`PF04567.23`	RNA_pol_Rpb2_5	693	736	5.2e-07	31.1
LXL04_034820	`PF00562.34`	RNA_pol_Rpb2_6	745	1114	4.2e-108	362.5
LXL04_034820	`PF04560.26`	RNA_pol_Rpb2_7	1116	1213	3.9e-27	95.2

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
`Q9LK40`	Arabidopsis thaliana	DNA-directed RNA polymerases IV and V subunit 2	63.015%	Swiss-Prot	strong database homology
`Q9LV32`	Arabidopsis thaliana	DNA-directed RNA polymerase D subunit 2b	65.275%	Swiss-Prot	strong database homology
`P38420`	Arabidopsis thaliana	DNA-directed RNA polymerase II subunit 2	33.950%	Swiss-Prot	moderate database homology

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