notch1b notch receptor 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: notch1bprovided by ZNC
Official Full Name: notch receptor 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-183
See related: Ensembl:ENSDARG00000052094 AllianceGenome:ZFIN:ZDB-GENE-990415-183
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: wu:fc55e11; etID309871.5
Summary: Predicted to enable calcium ion binding activity and signaling receptor activity. Involved in Notch signaling pathway. Acts upstream of or within several processes, including fin regeneration; nervous system development; and vasculature development. Predicted to be located in membrane and nucleus. Predicted to be part of protein-containing complex. Predicted to be active in plasma membrane. Is expressed in several structures, including cardiovascular system; digestive system; hematopoietic multipotent progenitor cell; nervous system; and trunk. Human ortholog(s) of this gene implicated in Adams-Oliver syndrome; adult T-cell leukemia/lymphoma; aortic valve disease 1; and congenital heart disease. Orthologous to human NOTCH1 (notch receptor 1). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (65679595..65782788, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (64997189..65103765, complement)

Chromosome 5 - NC_007116.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis.
Title: Antagonistic Activities of Vegfr3/Flt4 and Notch1b Fine-tune Mechanosensitive Signaling during Zebrafish Cardiac Valvulogenesis.
Reactivation of Notch signaling is required for cardiac valve regeneration.
Title: Reactivation of Notch signaling is required for cardiac valve regeneration.
Contractile and hemodynamic forces coordinate Notch1b-mediated outflow tract valve formation.
Title: Contractile and hemodynamic forces coordinate Notch1b-mediated outflow tract valve formation.
identified a 42-bp heart-specific enhancer near the NOTCH1 gene and further verified its functional targeting by NKX2-5.
Title: Identification of a 42-bp heart-specific enhancer of the notch1b gene in zebrafish embryos.
Results suggest that Notch signaling regulates glycolysis-related gene expression in a context-dependent manner in neural tissues at different developmental stages.
Title: Notch signaling regulates the expression of glycolysis-related genes in a context-dependent manner during embryonic development.
Notch signalling strength is quantitatively interpreted in different organ systems, and suggest a role for intercellular communication in regulating the output period of the segmentation clock by altering its spatial pattern.
Title: Faster embryonic segmentation through elevated Delta-Notch signalling.
Notch1a and Notch1b, are each required intrinsically to fate hematopoietic stem cells (HSCs), just prior to their emergence from aortic hemogenic endothelium.
Title: Discrete Notch signaling requirements in the specification of hematopoietic stem cells.
90 % of proliferating radial glia express notch1a, notch1b and notch3. In contrast, the proliferating non-glial populations of the dorsal telencephalon and hypothalamus rarely express notch3 and about half express notch1a/1b.
Title: Notch receptor expression in neurogenic regions of the adult zebrafish brain.
Notch1b is required for the maintenance of progenitor division and fate in pallial ventricular cells.
Title: Notch3 signaling gates cell cycle entry and limits neural stem cell amplification in the adult pallium.
a master role for Notch signaling in vertebrate mast cell development which establishes developmental origins of this lineage.
Title: The zebrafish reveals dependence of the mast cell lineage on Notch signaling in vivo.

Submit: New GeneRIF Correction See all GeneRIFs (12)

General gene information

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Markers

not1b (e-PCR)
- UniSTS:187003

Notch (e-PCR)
- UniSTS:205710

fc55e11 (e-PCR)
- UniSTS:189361

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in Notch signaling pathway	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within angiogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within artery development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal aorta development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in establishment or maintenance of epithelial cell apical/basal polarity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hematopoietic stem cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lymphangiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuronal stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of developmental process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rhombomere boundary formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within ventral spinal cord interneuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: neurogenic locus notch homolog protein 1b

Names: notch 1b; notch homolog 1b; notch receptor protein 1b

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_131302.2 → NP_571377.2 neurogenic locus notch homolog protein 1b precursor

See identical proteins and their annotated locations for NP_571377.2

Status: PROVISIONAL

Source sequence(s)

AY805407

UniProtKB/TrEMBL

A0PGH6

Related

ENSDARP00000050854.3, ENSDART00000050855.4

Conserved Domains (10) summary

smart00004
Location:1498 → 1538

NL; Domain found in Notch and Lin-12

cd00054
Location:925 → 961

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd00204
Location:1900 → 2012

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

pfam00008
Location:1043 → 1073

EGF; EGF-like domain

pfam00066
Location:1464 → 1499

Notch; LNR domain

pfam06816
Location:1544 → 1595

NOD; NOTCH protein

pfam07684
Location:1650 → 1707

NODP; NOTCH protein

pfam11936
Location:2387 → 2450

DUF3454; Domain of unknown function (DUF3454)

pfam12796
Location:1910 → 2003

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:1857 → 1903

ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007116.7 Reference GRCz11 Primary Assembly

Range

65679595..65782788 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005168649.5 → XP_005168706.1 neurogenic locus notch homolog protein 1b isoform X1

UniProtKB/TrEMBL

A0A8M2BFY6

Related

ENSDARP00000105460.2, ENSDART00000130888.4

Conserved Domains (10) summary

smart00004
Location:1515 → 1555

NL; Domain found in Notch and Lin-12

cd00054
Location:866 → 902

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd00204
Location:1917 → 2029

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

pfam00008
Location:1060 → 1090

EGF; EGF-like domain

pfam00066
Location:1481 → 1516

Notch; LNR domain

pfam06816
Location:1561 → 1612

NOD; NOTCH protein

pfam07684
Location:1667 → 1724

NODP; NOTCH protein

pfam11936
Location:2404 → 2467

DUF3454; Domain of unknown function (DUF3454)

pfam12796
Location:1927 → 2020

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:1874 → 1920

ANK; ANK repeat [structural motif]