ama-1 DNA-directed RNA polymerase II subunit RPB1 [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: ama-1
Gene description: DNA-directed RNA polymerase II subunit RPB1
Primary source: WormBase:WBGene00000123
Locus tag: CELE_F36A4.7
See related: AllianceGenome:WB:WBGene00000123
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Contributes to RNA polymerase II activity. Involved in several processes, including mRNA transcription by RNA polymerase II; positive regulation of gastrulation; and positive regulation of transcription, DNA-templated. Located in nucleus and transcriptionally active chromatin. Is expressed in several structures, including Z2; Z3; alimentary system; muscular system; and nervous system. Orthologous to human POLR2A (RNA polymerase II subunit A). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See ama-1 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 13

Sequence:: Chromosome: IV; NC_003282.8 (4248070..4258169)

Chromosome IV - NC_003282.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003282.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

F36A4.8 (e-PCR)
- UniSTS:316740

F36A4.7 (e-PCR)
- UniSTS:310149

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables DNA-directed 5'-3' RNA polymerase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
contributes_to RNA polymerase II activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to RNA polymerase II activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryo development ending in birth or egg hatching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of DNA-directed RNA polymerase complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II, core complex	IBA Inferred from Biological aspect of Ancestor more info
located_in chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
part_of euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear lumen	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-directed RNA polymerase II subunit RPB1

NP_500523.4

Partially confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003282.8 Reference assembly

Range

4248070..4258169

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_068122.9 → NP_500523.4 DNA-directed RNA polymerase II subunit RPB1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_500523.4

Status: REVIEWED

UniProtKB/Swiss-Prot

P16356, Q20090

Conserved Domains (8) summary

cd02584
Location:1053 → 1468

RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

smart01104
Location:1493 → 1584

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

PRK08566
Location:7 → 893

PRK08566; DNA-directed RNA polymerase subunit A'; Validated

cd02733
Location:17 → 870

RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain

pfam04992
Location:890 → 1073

RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6

pfam04998
Location:824 → 1420

RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5

pfam09786
Location:1735 → 1828

CytochromB561_N; Cytochrome B561, N terminal

pfam11914
Location:1746 → 1837

DUF3432; Domain of unknown function (DUF3432)