LXL04_031397 | RubberDandelionOmics

Gene overview

LXL04_031397

Reference: OH-1004 Chr: Chr07 Coordinates: 5388527-5395212 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5514 bp · LXL04_031397|LXL04_031397|OH1004|cDNA

ATGGATATACGGTTCCCTCACTCTCCAGCAGAAGTTGCAAAAGTCCGGCTGGTTCAGTTCGGCATCCTCAGTCCTGATGAAATTAGACAAATGTCTGTCGTGCATATAGAGCATGGCGAAACGACAGAAAGGGGGAAGCCAAAGGTAGCTGGACTTAGTGACCCAAGGCTTGGGACAATCGATAGGAAGATGAAATGCGAGACATGTATGGCAAATATGGCCGAGTGCCCTGGTCATTTTGGGCATCTCGAGCTTGCAAA...

CDS

Download CDS FASTA

5514 bp · LXL04_031397|LXL04_031397|OH1004|CDS

ATGGATATACGGTTCCCTCACTCTCCAGCAGAAGTTGCAAAAGTCCGGCTGGTTCAGTTCGGCATCCTCAGTCCTGATGAAATTAGACAAATGTCTGTCGTGCATATAGAGCATGGCGAAACGACAGAAAGGGGGAAGCCAAAGGTAGCTGGACTTAGTGACCCAAGGCTTGGGACAATCGATAGGAAGATGAAATGCGAGACATGTATGGCAAATATGGCCGAGTGCCCTGGTCATTTTGGGCATCTCGAGCTTGCAAA...

Protein

Download Protein FASTA

1837 aa · LXL04_031397|LXL04_031397|OH1004|PROTEIN

MDIRFPHSPAEVAKVRLVQFGILSPDEIRQMSVVHIEHGETTERGKPKVAGLSDPRLGTIDRKMKCETCMANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFNCSKILADEEDHKFKQAQKIRNPKNRLKKILDACKSKTKCDGGDEIDSQNQDTDEPVKKSRGGCGAQQPKITIEGMKMVAEYKLQKKKSDDSEQLPEPAERKQQLSAEKVLSVLKRVSDEDCLLLGLNPKYARPDWMILQVLPIPPPPVRPSV...

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_031397`
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_031397

Location Chr07:5388527-5395212 (+)

Description Similar to NRPB1: DNA-directed RNA polymerase II subunit RPB1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g35800`	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_031397 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006366 transcription by RNA polymerase II Biological Process

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

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0042789 mRNA transcription by RNA polymerase II Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0000791 euchromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005665 RNA polymerase II, core complex Cellular Component

GO:0005700 polytene chromosome Cellular Component

GO:0005703 polytene chromosome puff Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009506 plasmodesma Cellular Component

KEGG gene cross-reference

ath:AT4G35800

bta:282312

ddi:DDB_G0279193

dme:Dmel_CG1554

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.

Nucleus0.862

Rank 1 · LXL04_031397 · OH-1004

Cytoplasm0.193

Rank 2 · LXL04_031397 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_031397 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_031397 · OH-1004

Mitochondrion0.015

Rank 5 · LXL04_031397 · 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.

PF04997.18RNA_pol_Rpb1_114-269 aa

PF04997.18RNA_pol_Rpb1_1294-375 aa

PF00623.26RNA_pol_Rpb1_2377-551 aa

PF04983.24RNA_pol_Rpb1_3554-718 aa

PF05000.23RNA_pol_Rpb1_4745-849 aa

PF04998.23RNA_pol_Rpb1_5856-1446 aa

PF04992.20RNA_pol_Rpb1_6922-1106 aa

PF04990.18RNA_pol_Rpb1_71191-1325 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031397	`PF04997.18`	RNA_pol_Rpb1_1	14	269	2.2e-108	363.0
LXL04_031397	`PF04997.18`	RNA_pol_Rpb1_1	294	375	2.2e-108	363.0
LXL04_031397	`PF00623.26`	RNA_pol_Rpb1_2	377	551	3.4e-70	236.3
LXL04_031397	`PF04983.24`	RNA_pol_Rpb1_3	554	718	4.9e-52	176.8
LXL04_031397	`PF05000.23`	RNA_pol_Rpb1_4	745	849	9e-39	132.4
LXL04_031397	`PF04998.23`	RNA_pol_Rpb1_5	856	1446	3.7e-103	345.3
LXL04_031397	`PF04992.20`	RNA_pol_Rpb1_6	922	1106	2.6e-68	230.3
LXL04_031397	`PF04990.18`	RNA_pol_Rpb1_7	1191	1325	1.2e-53	181.5

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
`P18616`	Arabidopsis thaliana	DNA-directed RNA polymerase II subunit RPB1	80.130%	Swiss-Prot	strong database homology

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