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

Gene ID: 401115, updated on 5-Mar-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 be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
4p16.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2036554..2043964)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2034123..2042451)
105.20220307 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
  • 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. 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
  3. 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
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article
  5. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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

Process Evidence Code Pubs
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
NELL2-interacting cell ontogeny regulator 1; neuropeptide-like protein C4orf48
Names
NELL2-interacting cofactor for lumicrine signalling
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_2023_10

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  neuropeptide-like protein C4orf48 isoform X1

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

  2. XM_011513471.3 → XP_011511773.1  neuropeptide-like protein C4orf48 isoform X2

    See identical proteins and their annotated locations for XP_011511773.1

  3. XM_017008190.2 → XP_016863679.1  neuropeptide-like protein C4orf48 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  neuropeptide-like protein C4orf48 isoform X2

  2. XM_054349984.1 → XP_054205959.1  neuropeptide-like protein C4orf48 isoform X1

  3. XM_054349985.1 → XP_054205960.1  neuropeptide-like protein C4orf48 isoform X3

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

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