lin-42 PAS domain-containing protein;Period protein homolog lin-42 [Caenorhabditis elegans] - Gene

Summary

Go to the top of the page Help

Official Symbol: lin-42
Official Full Name: PAS domain-containing protein;Period protein homolog lin-42
Primary source: WormBase:WBGene00018572
Locus tag: CELE_F47F6.1
See related: AllianceGenome:WB:WBGene00018572
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: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in negative regulation of dauer larval development; negative regulation of pri-miRNA transcription by RNA polymerase II; and regulation of development, heterochronic. Located in cytoplasm and nucleus. Is expressed in several structures, including H1L.app; H1R.app; H2L.ppp; hypodermal cell; and pharynx. Human ortholog(s) of this gene implicated in advanced sleep phase syndrome; advanced sleep phase syndrome 1; and advanced sleep phase syndrome 3. Orthologous to several human genes including PER2 (period circadian regulator 2). [provided by Alliance of Genome Resources, Apr 2022]
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help

Location:: chromosome: II

Exon count:: 11

Sequence:: Chromosome: II; NC_003280.10 (1233236..1252359, complement)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans.
Title: Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans.
Temporal scaling in C. elegans larval development.
Title: Temporal scaling in C. elegans larval development.
These results establish a new role for the conserved, important Period protein homolog LIN-42 in regulating early germline development.
Title: The Period protein homolog LIN-42 regulates germline development in C. elegans.
The method was validated with a lin-42 mutant strain that shows delayed development relative to wild-type animals and with a daf-2 mutant that shows an extended second larval stage
Title: A High-Throughput Method for the Analysis of Larval Developmental Phenotypes in Caenorhabditis elegans.
A key function of lin-42 in developmental timing is to dampen pri-miRNAs levels, preventing their premature expression as mature miRNAs.
Title: Caenorhabditis elegans period homolog lin-42 regulates the timing of heterochronic miRNA expression.
lin-42 functions to negatively regulate the transcriptional output of multiple miRNAs and mRNAs and therefore coordinates the expression levels of genes that dictate temporal cell fate
Title: LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription.
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Title: The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Inactivation of the heterochronic gene lin-42a leads to arrhythmic molts and abnormal epidermal stem cell dynamics. Oscillatory expression in the epidermis peaks during the molts; forced expression leads to anachronistic larval molts and adult lethargy.
Title: LIN-42/PERIOD controls cyclical and developmental progression of C. elegans molts.
The C. elegans developmental timing protein LIN-42 regulates diapause in response to environmental cues.
Title: The C. elegans developmental timing protein LIN-42 regulates diapause in response to environmental cues.
LIN-42 has a dynamic expression pattern; its levels oscillate relative to the molts during postembryonic development.
Title: Novel heterochronic functions of the Caenorhabditis elegans period-related protein LIN-42.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

F47F6.1 (e-PCR)
- UniSTS:322147

F47F6.2 (e-PCR)
- UniSTS:311655

STS2-107 (e-PCR)
- UniSTS:241772

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of dauer larval development	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of dauer larval development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of dauer larval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of miRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of development, heterochronic	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	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

Go to the top of the page Help

Preferred Names: PAS domain-containing protein;Period protein homolog lin-42

NP_001022176.1

Confirmed by transcript evidence

NP_001022177.1

Confirmed by transcript evidence

NP_001022178.1

Confirmed by transcript evidence

NP_001309559.1

Partially confirmed by transcript evidence

NP_001309560.1

Confirmed by transcript evidence

NP_001309561.1

Partially confirmed by transcript evidence

NP_001309562.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

Genome Annotation

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

Reference assembly

Genomic

NC_003280.10 Reference assembly

Range

1233236..1252359 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001027006.7 → NP_001022177.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022177.1

Status: REVIEWED

UniProtKB/Swiss-Prot

H2L053, P91313, Q65ZG8

Conserved Domains (2) summary

cd00130
Location:168 → 271

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam14598
Location:169 → 271

PAS_11; PAS domain
NM_001027005.4 → NP_001022176.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022176.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q65ZG8
NM_001322704.3 → NP_001309559.1 PAS domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MAY5

Conserved Domains (1) summary

cd00130
Location:225 → 328

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
NM_001322705.3 → NP_001309560.1 Period protein homolog lin-42 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MAT8
NM_001322706.3 → NP_001309562.1 Period protein homolog lin-42 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MCB3
NM_001027007.3 → NP_001022178.1 Period protein homolog lin-42 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022178.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q65ZG8

Conserved Domains (2) summary

cd00130
Location:168 → 271

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam14598
Location:169 → 271

PAS_11; PAS domain
NM_001322707.3 → NP_001309561.1 PAS domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A131MBE1

Conserved Domains (1) summary

cd00130
Location:225 → 328

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...