LXL04_027604 | RubberDandelionOmics

Gene overview

LXL04_027604

Reference: OH-1004 Chr: Chr06 Coordinates: 19973708-19982325 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5817 bp · LXL04_027604|LXL04_027604|OH1004|cDNA

ATGATGGAAGAAAATCCAAATCCTGCTGTTTTAGAAGGGAAGATTACGGGGATTAGCTTTTCATTGGCCACGCAACAAGAAATTTGCTTGGCTTCAATTAGTGATTGCCCCATTAGCCATGCAAGCCAGCTTTCAAACCCCTTTCTTGGACTTCCTCTAGAAGTTGGGAAGTGTGAATCTTGTGGTACAGCTGAACCAGGCAAATGTGAAGGTCATTTCGGGTATATAGAGTTGCCAATTCCAATATATCATCCGTCTCA...

CDS

Download CDS FASTA

5817 bp · LXL04_027604|LXL04_027604|OH1004|CDS

ATGATGGAAGAAAATCCAAATCCTGCTGTTTTAGAAGGGAAGATTACGGGGATTAGCTTTTCATTGGCCACGCAACAAGAAATTTGCTTGGCTTCAATTAGTGATTGCCCCATTAGCCATGCAAGCCAGCTTTCAAACCCCTTTCTTGGACTTCCTCTAGAAGTTGGGAAGTGTGAATCTTGTGGTACAGCTGAACCAGGCAAATGTGAAGGTCATTTCGGGTATATAGAGTTGCCAATTCCAATATATCATCCGTCTCA...

Protein

Download Protein FASTA

1938 aa · LXL04_027604|LXL04_027604|OH1004|PROTEIN

MMEENPNPAVLEGKITGISFSLATQQEICLASISDCPISHASQLSNPFLGLPLEVGKCESCGTAEPGKCEGHFGYIELPIPIYHPSHLTELKRILSLICLKCLKFKNRRLQNKNSGMLERVLTVCCDEAACVTISEEKKEDGASYLQLKVPSKTCKDGLWDFLDRYGYRYGHGHKRPLLPSEVLVMLKKISESTKKKLAGRGCYFQEGYIMQHLPIPPNCLSTPDVSDGMNVMSSDISMTMLKKVLRQVEIIKSSRSGSP...

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_027604`
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_027604

Location Chr06:19973708-19982325 (+)

Description Similar to NRPE1: DNA-directed RNA polymerase V subunit 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40030`	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 The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.2006 · DOI: 10.1016/j.cell.2006.05.031 PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.2008 · DOI: 10.1073/pnas.0709632105 NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03525.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027604 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

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

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006370 7-methylguanosine mRNA capping Biological Process

GO:0019985 translesion synthesis Biological Process

GO:0030422 siRNA processing Biological Process

GO:0030643 intracellular phosphate ion homeostasis Biological Process

GO:0033120 positive regulation of RNA splicing Biological Process

KEGG gene cross-reference

ago:AGOS_ADR086C

ath:AT2G40030

bta:282312

hsa:5430

spo:2540292

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.

Nucleus0.675

Rank 1 · LXL04_027604 · OH-1004

Cytoplasm0.278

Rank 2 · LXL04_027604 · OH-1004

Cell membrane0.073

Rank 3 · LXL04_027604 · OH-1004

Endoplasmic reticulum0.055

Rank 4 · LXL04_027604 · OH-1004

Mitochondrion0.047

Rank 5 · LXL04_027604 · 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.

PF04997.18RNA_pol_Rpb1_148-289 aa

PF00623.26RNA_pol_Rpb1_2324-477 aa

PF04983.24RNA_pol_Rpb1_3482-626 aa

PF04998.23RNA_pol_Rpb1_5754-1173 aa

PF11523.14DUF32231735-1809 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027604	`PF04997.18`	RNA_pol_Rpb1_1	48	289	5.5e-14	52.9
LXL04_027604	`PF00623.26`	RNA_pol_Rpb1_2	324	477	1e-35	124.1
LXL04_027604	`PF04983.24`	RNA_pol_Rpb1_3	482	626	3e-06	27.9
LXL04_027604	`PF04998.23`	RNA_pol_Rpb1_5	754	1173	3.7e-11	43.7
LXL04_027604	`PF11523.14`	DUF3223	1735	1809	6.4e-27	94.6

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
`Q5D869`	Arabidopsis thaliana	DNA-directed RNA polymerase V subunit 1	47.653%	Swiss-Prot	moderate database homology

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