LXL04_027241 | RubberDandelionOmics

Gene overview

LXL04_027241

Reference: OH-1004 Chr: Chr06 Coordinates: 11577053-11584214 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3729 bp · LXL04_027241|LXL04_027241|OH1004|cDNA

atggcgcccccagcaggtcaccactttggtcgctcacgaagagcaacccaccgatccttaggaaacccccggacaactggggtaaaacccggatgcatccaCCCAGGATCGAACACTGAACCTCCACTAGGAAAGTCGAGCTTTCCTAAGGATTTAGGTATGGATTTGGAAGAAGAGTATGATCAAGGATACAACGATGAGGAAGAAGACATAACCCAAGAGGATGCTTGGGCAGTTATCAGTTCTTATTTCGAAGAAAA...

CDS

Download CDS FASTA

3729 bp · LXL04_027241|LXL04_027241|OH1004|CDS

ATGGCGCCCCCAGCAGGTCACCACTTTGGTCGCTCACGAAGAGCAACCCACCGATCCTTAGGAAACCCCCGGACAACTGGGGTAAAACCCGGATGCATCCACCCAGGATCGAACACTGAACCTCCACTAGGAAAGTCGAGCTTTCCTAAGGATTTAGGTATGGATTTGGAAGAAGAGTATGATCAAGGATACAACGATGAGGAAGAAGACATAACCCAAGAGGATGCTTGGGCAGTTATCAGTTCTTATTTCGAAGAAAA...

Protein

Download Protein FASTA

1242 aa · LXL04_027241|LXL04_027241|OH1004|PROTEIN

MAPPAGHHFGRSRRATHRSLGNPRTTGVKPGCIHPGSNTEPPLGKSSFPKDLGMDLEEEYDQGYNDEEEDITQEDAWAVISSYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQPDFAETIYKISFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVSKRAIKKGHDGEEVTETQDFAKVFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNH...

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_027241`
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_027241

Location Chr06:11577053-11584214 (-)

Description Similar to RPB2: DNA-directed RNA polymerase II subunit RPB2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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_027241 · 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:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0035196 miRNA processing Biological Process

GO:0000781 chromosome, telomeric region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005665 RNA polymerase II, core complex Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT4G21710

bta:538184

ddi:DDB_G0288257

hsa:5431

sly:544278

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.

Nucleus0.948

Rank 1 · LXL04_027241 · OH-1004

Cytoplasm0.074

Rank 2 · LXL04_027241 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_027241 · OH-1004

Mitochondrion0.016

Rank 4 · LXL04_027241 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_027241 · 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.

PF04563.21RNA_pol_Rpb2_188-497 aa

PF04561.20RNA_pol_Rpb2_2258-449 aa

PF04565.22RNA_pol_Rpb2_3522-586 aa

PF04566.19RNA_pol_Rpb2_4621-682 aa

PF04567.23RNA_pol_Rpb2_5707-758 aa

PF00562.34RNA_pol_Rpb2_6765-1135 aa

PF04560.26RNA_pol_Rpb2_71137-1228 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027241	`PF04563.21`	RNA_pol_Rpb2_1	88	497	2.4e-78	263.0
LXL04_027241	`PF04561.20`	RNA_pol_Rpb2_2	258	449	4.9e-55	186.9
LXL04_027241	`PF04565.22`	RNA_pol_Rpb2_3	522	586	4.8e-25	88.2
LXL04_027241	`PF04566.19`	RNA_pol_Rpb2_4	621	682	1.4e-23	83.5
LXL04_027241	`PF04567.23`	RNA_pol_Rpb2_5	707	758	4.5e-18	66.6
LXL04_027241	`PF00562.34`	RNA_pol_Rpb2_6	765	1135	6.5e-141	470.5
LXL04_027241	`PF04560.26`	RNA_pol_Rpb2_7	1137	1228	1.8e-36	125.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`P38420`	Arabidopsis thaliana	DNA-directed RNA polymerase II subunit 2	93.510%	Swiss-Prot	strong database homology

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