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    NICOL1 NELL2 interacting cell ontogeny regulator 1 [ Homo sapiens (human) ]

    Gene ID: 401115, updated on 3-Nov-2024

    Summary

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    Official Symbol
    NICOL1provided by HGNC
    Official Full Name
    NELL2 interacting cell ontogeny regulator 1provided by HGNC
    Primary source
    HGNC:HGNC:34437
    See related
    Ensembl:ENSG00000243449 MIM:614690; AllianceGenome:HGNC:34437
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NICOL; C4orf48; CHR4_55
    Summary
    Predicted to enable mRNA 3'-UTR binding activity. Predicted to be involved in 3'-UTR-mediated mRNA stabilization. Predicted to be located in extracellular space and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in colon (RPKM 2.0), small intestine (RPKM 1.6) and 10 other tissues See more
    Orthologs
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    Genomic context

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    See NICOL1 in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2036554..2043964)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2034123..2042451)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2043722..2045691)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene nuclear receptor binding SET domain protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1993535-1994374 Neighboring gene small Cajal body-specific RNA 22 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1999747-2000246 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2010384-2010884 Neighboring gene uncharacterized LOC124900839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15152 Neighboring gene microRNA 943 Neighboring gene negative elongation factor complex member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2042861-2043362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2068259-2068872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2071383-2072064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2077922-2078535 Neighboring gene HBS1 like translational GTPase pseudogene Neighboring gene N-acetyltransferase 8 like Neighboring gene DNA polymerase nu

    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 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. C4ORF48, a gene from the Wolf-Hirschhorn syndrome critical region, encodes a putative neuropeptide and is expressed during neocortex and cerebellar development. Endele S, et al. Neurogenetics, 2011 May. PMID 21287218
    2. The secreted micropeptide C4orf48 enhances renal fibrosis via an RNA-binding mechanism. Yang J, et al. J Clin Invest, 2024 Apr 16. PMID 38625739, Free PMC Article
    3. A small secreted protein NICOL regulates lumicrine-mediated sperm maturation and male fertility. Kiyozumi D, et al. Nat Commun, 2023 Apr 24. PMID 37095084, Free PMC Article
    4. Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Castelo R, et al. Nucleic Acids Res, 2005. PMID 15809229, Free PMC Article
    5. Mapping Extracellular Protein-Protein Interactions Using Extracellular Proximity Labeling (ePL). Peeney D, et al. J Proteome Res, 2024 Oct 4. PMID 39238192,

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The secreted micropeptide C4orf48 enhances renal fibrosis via an RNA-binding mechanism.
      Title: The secreted micropeptide C4orf48 enhances renal fibrosis via an RNA-binding mechanism.
    2. C4Orf48 probably encodes a novel neuropeptide, which, if hemizygously deleted, may be involved in the observed intellectual and fine motor disabilities and thus in the overall neurological aspects of Wolf-Hirschhorn syndrome.
      Title: C4ORF48, a gene from the Wolf-Hirschhorn syndrome critical region, encodes a putative neuropeptide and is expressed during neocortex and cerebellar development.
    Submit: New GeneRIF Correction

    Phenotypes

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    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables mRNA 3'-UTR binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transferrin receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in 3'-UTR-mediated mRNA stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    NELL2-interacting cell ontogeny regulator 1
    Names
    NELL2-interacting cofactor for lumicrine signaling
    NELL2-interacting cofactor for lumicrine signalling
    neuropeptide-like protein C4orf48
    NP_001135408.3
    NP_001161715.3
    XP_011511771.1
    XP_011511773.1
    XP_016863679.1
    XP_047300254.1
    XP_054205959.1
    XP_054205960.1

    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)

    1. NM_001141936.3 → NP_001135408.3  NELL2-interacting cell ontogeny regulator 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AL132868
      Consensus CDS
      CCDS47000.2
      UniProtKB/Swiss-Prot
      B6ZDN0, B7ZBI7, B7ZBI8, Q5BLP8, X6RBU3
      Related
      ENSP00000386528.1, ENST00000409860.1
      Conserved Domains (1) summary
      pfam15161
      Location:34 → 93
      Neuropep_like; Neuropeptide-like

    2. NM_001168243.4 → NP_001161715.3  NELL2-interacting cell ontogeny regulator 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL132868
      Consensus CDS
      CCDS47000.2
      UniProtKB/Swiss-Prot
      B6ZDN0, B7ZBI7, B7ZBI8, Q5BLP8, X6RBU3
      Related
      ENSP00000386807.5, ENST00000409248.10
      Conserved Domains (1) summary
      pfam15161
      Location:34 → 93
      Neuropep_like; Neuropeptide-like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      2036554..2043964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513469.4 → XP_011511771.1  NELL2-interacting cell ontogeny regulator 1 isoform X1

      Conserved Domains (1) summary
      pfam15161
      Location:90 → 149
      Neuropep_like; Neuropeptide-like

    2. XM_011513471.3 → XP_011511773.1  NELL2-interacting cell ontogeny regulator 1 isoform X2

      See identical proteins and their annotated locations for XP_011511773.1

    3. XM_017008190.2 → XP_016863679.1  NELL2-interacting cell ontogeny regulator 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      2034123..2042451
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444298.1 → XP_047300254.1  NELL2-interacting cell ontogeny regulator 1 isoform X2

    2. XM_054349984.1 → XP_054205959.1  NELL2-interacting cell ontogeny regulator 1 isoform X1

    3. XM_054349985.1 → XP_054205960.1  NELL2-interacting cell ontogeny regulator 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5BLP8.3 GenPept UniProtKB/Swiss-Prot:Q5BLP8

    Gene LinkOut

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