Nelfb negative elongation factor complex member B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nelfbprovided by MGI
Official Full Name: negative elongation factor complex member Bprovided by MGI
Primary source: MGI:MGI:1931035
See related: Ensembl:ENSMUSG00000013465 AllianceGenome:MGI:1931035
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cobra1; Nelf-b; A730008L03Rik
Summary: This gene encodes subunit B of a metazoan-specific, four-subunit protein complex that regulates promoter-proximal pausing of RNA polymerase II. RNA polymerase II pausing is thought to be important for coordination of gene transcription during embryonic development and stress responses. Consistently, disruption of this gene in mouse causes inner cell mass deficiency and embryonic lethality. In addition, this gene is required for maintenance of mouse embryonic stem cells by preventing expression of developmental genes. In adult mice, conditional deletion of this gene results in cardiomyopathy and impaired response to cardiac stress. Multiple protein isoforms are encoded through the use of a non-AUG (CUG) initiation codon and an alternative downstream AUG initiation codon. In addition, alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
Expression: Ubiquitous expression in limb E14.5 (RPKM 19.3), CNS E11.5 (RPKM 18.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 A3; 2 17.06 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (25089724..25101501, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (25199712..25211489, complement)

Chromosome 2 - NC_000068.8 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: 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?

An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing.
Title: An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing.
BRCA1 Interacting Protein COBRA1 Facilitates Adaptation to Castrate-Resistant Growth Conditions.
Title: BRCA1 Interacting Protein COBRA1 Facilitates Adaptation to Castrate-Resistant Growth Conditions.
This study uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription program during mammary gland development.
Title: Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development.
both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG.
Title: Translational Initiation at a Non-AUG Start Codon for Human and Mouse Negative Elongation Factor-B.
Human and mouse Nelfb encode proteins translated from a non-AUG (CUG) start codon. The majority of mouse tissues examined express the isoform translated from the CUG start codon, but a small number of tissues also express a shorter isoform of the same apparent size as the AUG-initiated isoform.
Title: Translational Initiation at a Non-AUG Start Codon for Human and Mouse Negative Elongation Factor-B.
Cobra1 Is Required for TrkC-Induced Apoptosis.
Title: The dependence receptor TrkC triggers mitochondria-dependent apoptosis upon Cobra-1 recruitment.
genetic and genomic studies provide new physiological and molecular insight into Nelf-mediated pol II pausing.
Title: Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth.
findings also indicate that Cobra1 helps maintain the undifferentiated state of mESCs by preventing unscheduled expression of developmental genes
Title: Mouse cofactor of BRCA1 (Cobra1) is required for early embryogenesis.

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Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH136194 (e-PCR)
- UniSTS:210189

Cobra1 (e-PCR), detects polymorphism
- UniSTS:526749

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NELF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NELF complex	ISO Inferred from Sequence Orthology more info
part_of NELF complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrial outer membrane	TAS Traceable Author Statement more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: negative elongation factor B

Names: cofactor of BRCA1; negative elongation factor complex member B, Cobra1; ortholog of human cofactor of BRCA1 (COBRA1)

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_001310157.1 → NP_001297086.1 negative elongation factor B isoform 2

See identical proteins and their annotated locations for NP_001297086.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses alternate splice sites in the 5' coding region, which results in use of a downstream start codon compared to variant 1. It encodes isoform 2, which has a shorter N-terminus than isoform 1.

Source sequence(s)

AI843129, AK173124, AL732309, CJ100279, CX241076

UniProtKB/Swiss-Prot

A0A0X1KG62, Q69ZP4, Q8C4Y3, Q99J41, Q9JJA5

Related

ENSMUST00000128876.8

Conserved Domains (1) summary

pfam06209
Location:2 → 473

COBRA1; Cofactor of BRCA1 (COBRA1)
NM_021393.3 → NP_067368.3 negative elongation factor B isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer isoform (1), which is translated using a non-AUG (CUG) start codon.

Source sequence(s)

AI843129, AK173124, AL732309, CJ100279

Consensus CDS

CCDS15751.2

UniProtKB/TrEMBL

A0A5H1ZRL3

Related

ENSMUSP00000057731.10, ENSMUST00000059849.15

Conserved Domains (1) summary

pfam06209
Location:155 → 626

COBRA1; Cofactor of BRCA1 (COBRA1)