LXL04_000311 | RubberDandelionOmics

Gene overview

LXL04_000311

Reference: OH-1004 Chr: Chr01 Coordinates: 5794083-5795846 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

702 bp · LXL04_000311|LXL04_000311|OH1004|cDNA

ATGGACGAGAATGGCGGAGATGCCATGGAAACGGAGATGAGTAACGGTGGCGGAGGGACGACGGGGCTGTGTTTGAGCAGCTTAGTTGACGAAGGTAGCACCGAGAGTCACCGATACTACCTTTCACGTAGAACTCTGTTAGAGATGCTCAGAGACAGAGGTTACGATGTCTCCAATTCGGAAATCGAGCTCACTCTCCAGCAGTTCCGGGAACTCCATGGTCAAGTTGTCGACGTTGACCGTCTTCGAATCAGCGCTTC...

CDS

Download CDS FASTA

702 bp · LXL04_000311|LXL04_000311|OH1004|CDS

ATGGACGAGAATGGCGGAGATGCCATGGAAACGGAGATGAGTAACGGTGGCGGAGGGACGACGGGGCTGTGTTTGAGCAGCTTAGTTGACGAAGGTAGCACCGAGAGTCACCGATACTACCTTTCACGTAGAACTCTGTTAGAGATGCTCAGAGACAGAGGTTACGATGTCTCCAATTCGGAAATCGAGCTCACTCTCCAGCAGTTCCGGGAACTCCATGGTCAAGTTGTCGACGTTGACCGTCTTCGAATCAGCGCTTC...

Protein

Download Protein FASTA

233 aa · LXL04_000311|LXL04_000311|OH1004|PROTEIN

MDENGGDAMETEMSNGGGGTTGLCLSSLVDEGSTESHRYYLSRRTLLEMLRDRGYDVSNSEIELTLQQFRELHGQVVDVDRLRISASHVSEPDNKILAVFCGTGVVKVNAIRWITTQIMNKESLSRLIIVVQSHITNQALKAVDLFPFKVDIFQITDLLVNITKHVLKPKHRVITDVEKAKLLKKFNLNEKQLPRMSQKDAIAQYYGLEKGQVIEVTYNGEITGLHVTYRCIW

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_000311`
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_000311

Location Chr01:5794083-5795846 (+)

Description Similar to NRPE5A: DNA-directed RNA polymerase V subunit 5A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g57080`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242
`At2g41340`	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
`At3g54490`	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
`At3g22320`	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_000311 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006362 transcription elongation by RNA polymerase I Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0042797 tRNA transcription by RNA polymerase III Biological Process

GO:0000418 RNA polymerase IV complex Cellular Component

GO:0000419 RNA polymerase V complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005665 RNA polymerase II, core complex Cellular Component

GO:0005666 RNA polymerase III complex Cellular Component

GO:0005736 RNA polymerase I complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003899 DNA-directed RNA polymerase activity Molecular Function

KEGG gene cross-reference

ath:AT2G41340

ath:AT3G22320

ath:AT3G54490

ath:AT3G57080

cbr:CBG_12745

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.

Nucleus0.902

Rank 1 · LXL04_000311 · OH-1004

Cytoplasm0.185

Rank 2 · LXL04_000311 · OH-1004

Mitochondrion0.030

Rank 3 · LXL04_000311 · OH-1004

Cell membrane0.017

Rank 4 · LXL04_000311 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_000311 · 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.

PF03871.21RNA_pol_Rpb5_N34-117 aa

PF01191.25RNA_pol_Rpb5_C160-232 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000311	`PF03871.21`	RNA_pol_Rpb5_N	34	117	4.4e-22	79.3
LXL04_000311	`PF01191.25`	RNA_pol_Rpb5_C	160	232	1.7e-28	98.9

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
`Q9M1J2`	Arabidopsis thaliana	DNA-directed RNA polymerase V subunit 5A	60.550%	Swiss-Prot	strong database homology
`Q9ZVB9`	Arabidopsis thaliana	DNA-directed RNA polymerases IV and V subunit 5B	61.765%	Swiss-Prot	strong database homology
`Q9M1H8`	Arabidopsis thaliana	DNA-directed RNA polymerase V subunit 5C	47.368%	Swiss-Prot	moderate database homology
`O81098`	Arabidopsis thaliana	DNA-directed RNA polymerases II and IV subunit 5A	36.000%	Swiss-Prot	moderate database homology

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