Nrl neural retina leucine zipper gene [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nrlprovided by MGI
Official Full Name: neural retina leucine zipper geneprovided by MGI
Primary source: MGI:MGI:102567
See related: Ensembl:ENSMUSG00000040632 AllianceGenome:MGI:102567
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: D14H14S46E
Summary: This gene encodes a member of the basic leucine zipper domain family of transcription factors. The encoded protein is preferentially expressed in the retina and is necessary for rod photoreceptor development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 14 C3; 14 28.19 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	14	NC_000080.7 (55756973..55762438, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	14	NC_000080.6 (55518978..55524981, complement)

Chromosome 14 - NC_000080.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina.
Title: Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina.
In the Nphp5-/- and cone-only Nphp5-/-; Nrl-/- mice, cone outer segments did not form, but mutant cones continued to express cone pigments in the inner segments without obvious signs of cone cell death.
Title: Rescue of cone function in cone-only Nphp5 knockout mouse model with Leber congenital amaurosis phenotype.
The Frmd4bTvrm222 allele was also found to suppress outer nuclear layer (ONL) rosettes in Nrl-/- mice. Fragmentation of the external limiting membrane (ELM), normally observed in rd7 and Nrl-/-mouse retinas, was absent in the presence of the Frmd4bTvrm222 allele
Title: An FRMD4B variant suppresses dysplastic photoreceptor lesions in models of enhanced S-cone syndrome and of Nrl deficiency.
that two photoreceptor-specific transcription factors, NRL and CRX, are master regulators of this program and are required for tumor maintenance in this subgroup
Title: NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma.
Following Nrl disruption, rods gain partial features of cones and present with improved survival in the presence of mutations in rod-specific genes, consequently preventing secondary cone degeneration. In three different mouse models of retinal degeneration, the treatment substantially improves rod survival and preserves cone function.
Title: Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice.
Nrl is posttranscriptionally regulated to facilitate the generation of other cell types in retina
Title: miR Cluster 143/145 Directly Targets Nrl and Regulates Rod Photoreceptor Development.
De novo assembly and alternative splicing analyses revealed previously unannotated rod-enriched transcripts and the role of NRL in transcript maturation.
Title: NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors.
Our studies reveal coregulation of coding and noncoding transcripts in rod photoreceptors by NRL and establish the framework for deciphering the function of ncRNAs during retinal development.
Title: Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL.
To explore dendritic stratification of OFF bipolar cells in the absence of rods, we made use of the 'cone-full' Nrl-/- mouse retina in which all photoreceptor precursor cells commit to a cone fate including those which would have become rods in wild-type retinas
Title: Dendritic stratification differs among retinal OFF bipolar cell types in the absence of rod photoreceptors.
CNGA3 expression restored cone function in in CNGA3-/-/Nrl-/- mice, an all-cone model of CNGA3 achromatopsia.
Title: Vitreal delivery of AAV vectored Cnga3 restores cone function in CNGA3-/-/Nrl-/- mice, an all-cone model of CNGA3 achromatopsia.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (5) 1 citation
Endonuclease-mediated (4)

General gene information

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Markers

Nrl (e-PCR), detects polymorphism
- UniSTS:536455

L14935 (e-PCR)
- UniSTS:160392

AW492574 (e-PCR)
- UniSTS:180634

Nrl (e-PCR), detects polymorphism
- UniSTS:144068

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables leucine zipper domain binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal rod cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retinal rod cell development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: neural retina-specific leucine zipper protein

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_001136074.3 → NP_001129546.1 neural retina-specific leucine zipper protein isoform 1

See identical proteins and their annotated locations for NP_001129546.1

Status: VALIDATED

Source sequence(s)

AC159002

Consensus CDS

CCDS27113.1

UniProtKB/Swiss-Prot

P54846

UniProtKB/TrEMBL

Q543Y0, Q8C8Y1

Related

ENSMUSP00000136445.2, ENSMUST00000178694.3

Conserved Domains (2) summary

cd14718
Location:154 → 223

bZIP_Maf_large; Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain

pfam08383
Location:67 → 101

Maf_N; Maf N-terminal region
NM_001271916.2 → NP_001258845.1 neural retina-specific leucine zipper protein isoform 1

See identical proteins and their annotated locations for NP_001258845.1

Status: VALIDATED

Source sequence(s)

AC159002

Consensus CDS

CCDS27113.1

UniProtKB/Swiss-Prot

P54846

UniProtKB/TrEMBL

Q543Y0, Q8C8Y1

Related

ENSMUSP00000054457.8, ENSMUST00000062232.15

Conserved Domains (2) summary

cd14718
Location:154 → 223

bZIP_Maf_large; Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain

pfam08383
Location:67 → 101

Maf_N; Maf N-terminal region
NM_001271917.2 → NP_001258846.1 neural retina-specific leucine zipper protein isoform 1

See identical proteins and their annotated locations for NP_001258846.1

Status: VALIDATED

Source sequence(s)

AC159002

Consensus CDS

CCDS27113.1

UniProtKB/Swiss-Prot

P54846

UniProtKB/TrEMBL

Q543Y0, Q8C8Y1

Related

ENSMUSP00000153933.2, ENSMUST00000228287.2

Conserved Domains (2) summary

cd14718
Location:154 → 223

bZIP_Maf_large; Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain

pfam08383
Location:67 → 101

Maf_N; Maf N-terminal region
NM_001424498.1 → NP_001411427.1 neural retina-specific leucine zipper protein isoform 2

Status: VALIDATED

Source sequence(s)

AC159002
NM_001424499.1 → NP_001411428.1 neural retina-specific leucine zipper protein isoform 3

Status: VALIDATED

Source sequence(s)

AC159002
NM_008736.4 → NP_032762.1 neural retina-specific leucine zipper protein isoform 1

See identical proteins and their annotated locations for NP_032762.1

Status: VALIDATED

Source sequence(s)

AC159002

Consensus CDS

CCDS27113.1

UniProtKB/Swiss-Prot

P54846

UniProtKB/TrEMBL

Q543Y0, Q8C8Y1

Related

ENSMUSP00000107035.2, ENSMUST00000111404.8

Conserved Domains (2) summary

cd14718
Location:154 → 223

bZIP_Maf_large; Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain

pfam08383
Location:67 → 101

Maf_N; Maf N-terminal region