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NSMF NMDA receptor synaptonuclear signaling and neuronal migration factor [ Homo sapiens (human) ]

Gene ID: 26012, updated on 5-Mar-2024

Summary

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Official Symbol
NSMFprovided by HGNC
Official Full Name
NMDA receptor synaptonuclear signaling and neuronal migration factorprovided by HGNC
Primary source
HGNC:HGNC:29843
See related
Ensembl:ENSG00000165802 MIM:608137; AllianceGenome:HGNC:29843
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HH9; NELF
Summary
The protein encoded by this gene is involved in guidance of olfactory axon projections and migration of luteinizing hormone-releasing hormone neurons. Defects in this gene are a cause of idiopathic hypogonadotropic hypogonadism (IHH). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
Expression
Broad expression in brain (RPKM 43.0), kidney (RPKM 13.5) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
9q34.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137447570..137459334, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149698122..149709468, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140342022..140353786, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene exonuclease 3'-5' domain containing 3 Neighboring gene uncharacterized LOC124902354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140323354-140324108 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140330497-140330751 Neighboring gene Sharpr-MPRA regulatory region 12030 Neighboring gene NADPH oxidase activator 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140343721-140344920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140346657-140347540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140347541-140348422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140349307-140350188 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140351970-140352667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140355491-140356424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140356425-140357357 Neighboring gene microRNA 7114 Neighboring gene patatin like phospholipase domain containing 7 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140377541-140378740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140389307-140389807 Neighboring gene 9q34.3 PNPLA7 recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140438353-140438854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140443963-140444464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20628 Neighboring gene uncharacterized LOC124902317 Neighboring gene mitochondrial ribosomal protein L41

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. JAK/STAT signaling pathway gene expression is reduced following Nelf knockdown in GnRH neurons. Ko EK, et al. Mol Cell Endocrinol, 2018 Jul 15. PMID 29050862
  2. Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription. Natarajan M, et al. J Biol Chem, 2013 Sep 6. PMID 23884411, Free PMC Article
  3. Nasal embryonic LHRH factor (NELF) mutations in patients with normosmic hypogonadotropic hypogonadism and Kallmann syndrome. Xu N, et al. Fertil Steril, 2011 Apr. PMID 21300340, Free PMC Article
  4. Characterization of the human nasal embryonic LHRH factor gene, NELF, and a mutation screening among 65 patients with idiopathic hypogonadotropic hypogonadism (IHH). Miura K, et al. J Hum Genet, 2004. PMID 15362570
  5. NSMF promotes the replication stress-induced DNA damage response for genome maintenance. Ju MK, et al. Nucleic Acids Res, 2021 Jun 4. PMID 33963872, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
    Title: NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
  2. NSMF promotes the replication stress-induced DNA damage response for genome maintenance.
    Title: NSMF promotes the replication stress-induced DNA damage response for genome maintenance.
  3. These findings suggest a role for NELF in the regulation of the JAK/STAT signaling pathway, which have important functions in GnRH neurons.
    Title: JAK/STAT signaling pathway gene expression is reduced following Nelf knockdown in GnRH neurons.
  4. The nuclear and non-nuclear NELF variant transcripts and proteins were identified, explaining variable NELF cellular localization.
    Title: Differential expression of nasal embryonic LHRH factor (NELF) variants in immortalized GnRH neuronal cell lines.
  5. a model in which NELF recruits Pcf11 and NCoR1-GPS2-HDAC3 to paused RNAP II, reinforcing repression of HIV transcription and establishing a critical checkpoint for HIV transcription and latency.
    Title: Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription.
  6. NELF is associated with normosmic idiopathic hypogonadotropic hypogonadism and Kallmann syndrome, either singly or in combination with a mutation in another gene.
    Title: Nasal embryonic LHRH factor (NELF) mutations in patients with normosmic hypogonadotropic hypogonadism and Kallmann syndrome.
  7. our findings implicate NELF as a nuclear protein involved in the developmental function of the reproductive axis.
    Title: NELF is a nuclear protein involved in hypothalamic GnRH neuronal migration.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Screening of autosomal gene deletions in patients with hypogonadotropic hypogonadism using multiplex ligation-dependent probe amplification: detection of a hemizygosis for the fibroblast growth factor receptor 1.
  9. 12% of Kallman syndrome males have KAL1 deletions, but intragenic deletions of the FGFR1, GNRH1, GNRHR, GPR54 and NELF genes are uncommon in Idiopathic hypogonadotropic hypogonadism/Kallman syndrome.
    Title: The prevalence of intragenic deletions in patients with idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC125369

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium-dependent protein binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in cellular response to amino acid stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to electrical stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to gonadotropin stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neuron migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in apical dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cortical cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of euchromatin ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear envelope ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear matrix ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
NMDA receptor synaptonuclear signaling and neuronal migration factor
Names
nasal embryonic LHRH factor
nasal embryonic luteinizing hormone-releasing hormone factor

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.

Genomic

  1. NG_021362.1 RefSeqGene

    Range
    5001..16765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130969.3 → NP_001124441.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform a

    See identical proteins and their annotated locations for NP_001124441.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AL365502
    Consensus CDS
    CCDS48069.1
    UniProtKB/Swiss-Prot
    Q2TB96, Q6X4V7, Q6X4V8, Q6X4V9, Q6X4W1, Q8N2M2, Q96SY1, Q9NPM4, Q9NPP3, Q9NPS3
    Related
    ENSP00000360530.3, ENST00000371475.9

  2. NM_001130970.2 → NP_001124442.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform c

    See identical proteins and their annotated locations for NP_001124442.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AW072125, AY255130, BM023184, CN306732
    Consensus CDS
    CCDS48068.1
    UniProtKB/Swiss-Prot
    Q6X4W1
    Related
    ENSP00000412007.1, ENST00000437259.5

  3. NM_001130971.2 → NP_001124443.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform d

    See identical proteins and their annotated locations for NP_001124443.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AW072125, AY255128, BC110498, BM023184, CN306732
    Consensus CDS
    CCDS48067.1
    UniProtKB/Swiss-Prot
    Q6X4W1
    Related
    ENSP00000360529.3, ENST00000371474.7

  4. NM_001178064.2 → NP_001171535.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform e

    See identical proteins and their annotated locations for NP_001171535.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (e) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AW072125, AY255131, BM023184, CN306732
    Consensus CDS
    CCDS55357.1
    UniProtKB/Swiss-Prot
    Q6X4W1
    Related
    ENSP00000360528.3, ENST00000371473.7

  5. NM_015537.5 → NP_056352.3  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform b

    See identical proteins and their annotated locations for NP_056352.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AW072125, AY255128, BC072412, BM023184, CN306732
    Consensus CDS
    CCDS7044.1
    UniProtKB/Swiss-Prot
    Q6X4W1
    Related
    ENSP00000265663.7, ENST00000265663.12

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137447570..137459334 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005266062.6 → XP_005266119.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X3

  2. XM_005266061.6 → XP_005266118.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X1

    See identical proteins and their annotated locations for XP_005266118.1

  3. XM_011518496.4 → XP_011516798.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X2

  4. XM_011518497.3 → XP_011516799.2  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X4

  5. XM_017014597.3 → XP_016870086.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149698122..149709468 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362656.1 → XP_054218631.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X3

  2. XM_054362654.1 → XP_054218629.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X1

  3. XM_054362655.1 → XP_054218630.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X2

  4. XM_054362658.1 → XP_054218633.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X5

  5. XM_054362657.1 → XP_054218632.1  NMDA receptor synaptonuclear signaling and neuronal migration factor isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6X4W1.1 GenPept UniProtKB/Swiss-Prot:Q6X4W1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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