Nelfe negative elongation factor complex member E, Rdbp [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nelfeprovided by MGI
Official Full Name: negative elongation factor complex member E, Rdbpprovided by MGI
Primary source: MGI:MGI:102744
See related: Ensembl:ENSMUSG00000024369 AllianceGenome:MGI:102744
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: RD; Rdbp; NELF-E; D17H6S45
Summary: Predicted to enable chromatin binding activity. Acts upstream of or within negative regulation of transcription elongation from RNA polymerase II promoter. Predicted to be located in nuclear body and plasma membrane. Predicted to be part of NELF complex. Is expressed in brain and early conceptus. Orthologous to human NELFE (negative elongation factor complex member E). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis adult (RPKM 47.2), CNS E11.5 (RPKM 20.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 B1; 17 18.4 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (35069367..35075348)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (34850391..34856372)

Chromosome 17 - NC_000083.7 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?

In every case, mice were found to be homozygous for the rd8 mutation, which informed the decision not to perform genotyping for this allele as a matter of routine, as the commercial mouse providers maintained their breeding schemes.
Title: A Population Study of Common Ocular Abnormalities in C57BL/6N rd8 Mice.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rdbp (e-PCR), detects polymorphism
- UniSTS:479245

AI255840 (e-PCR)
- UniSTS:181007

D17916 (e-PCR)
- UniSTS:124740

Cfb (e-PCR), detects polymorphism
- UniSTS:531085

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid 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 negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within 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 positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein modification process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

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 chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: negative elongation factor E

Names: RD RNA-binding protein; RNA-binding protein RD

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_001045863.1 → NP_001039328.1 negative elongation factor E

See identical proteins and their annotated locations for NP_001039328.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AI325150, AK147011, CX203833

Consensus CDS

CCDS28662.1

UniProtKB/Swiss-Prot

P19426, P97485, P97486, Q9CZN3

UniProtKB/TrEMBL

Q3UIA1

Related

ENSMUSP00000134272.2, ENSMUST00000173357.8

Conserved Domains (1) summary

cd12305
Location:254 → 328

RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins
NM_001045864.1 → NP_001039329.1 negative elongation factor E

See identical proteins and their annotated locations for NP_001039329.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein.

Source sequence(s)

AI325150, CN525174, CT025759, DV662511

Consensus CDS

CCDS28662.1

UniProtKB/Swiss-Prot

P19426, P97485, P97486, Q9CZN3

UniProtKB/TrEMBL

Q3UIA1

Related

ENSMUSP00000094956.5, ENSMUST00000097343.11

Conserved Domains (1) summary

cd12305
Location:254 → 328

RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins
NM_138580.2 → NP_613046.2 negative elongation factor E

See identical proteins and their annotated locations for NP_613046.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the shortest transcript. All variants encode the same protein.

Source sequence(s)

AI325150, AK131947, CX203833

Consensus CDS

CCDS28662.1

UniProtKB/Swiss-Prot

P19426, P97485, P97486, Q9CZN3

UniProtKB/TrEMBL

Q3UIA1

Related

ENSMUSP00000131195.3, ENSMUST00000165953.3

Conserved Domains (1) summary

cd12305
Location:254 → 328

RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins