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    HPCAL4 hippocalcin like 4 [ Homo sapiens (human) ]

    Gene ID: 51440, updated on 5-Mar-2024

    Summary

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    Official Symbol
    HPCAL4provided by HGNC
    Official Full Name
    hippocalcin like 4provided by HGNC
    Primary source
    HGNC:HGNC:18212
    See related
    Ensembl:ENSG00000116983 MIM:619211; AllianceGenome:HGNC:18212
    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
    HLP4
    Summary
    The protein encoded by this gene is highly similar to human hippocalcin protein and hippocalcin like-1 protein. It also has similarity to rat neural visinin-like Ca2+-binding protein-type 1 and 2 proteins. This encoded protein may be involved in the calcium-dependent regulation of rhodopsin phosphorylation. The transcript of this gene has multiple polyadenylation sites. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
    Expression
    Biased expression in brain (RPKM 58.2), adrenal (RPKM 5.9) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HPCAL4 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39678648..39691433, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39548023..39560837, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40144320..40157105, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hes related family bHLH transcription factor with YRPW motif like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 708 Neighboring gene Sharpr-MPRA regulatory region 4263 Neighboring gene 5'-nucleotidase, cytosolic IA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 709 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:40155381-40155607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40157484-40158074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40166488-40167140 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:40176174-40176931 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:40177551-40178246 Neighboring gene coiled-coil domain containing 25 pseudogene Neighboring gene RNA, U7 small nuclear 121 pseudogene

    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. Isolation of two human cDNAs, HLP3 and HLP4, homologous to the neuron-specific calcium-binding protein genes. Kobayashi M, et al. DNA Seq, 1998. PMID 10520747
    2. The EHEC-host interactome reveals novel targets for the translocated intimin receptor. Blasche S, et al. Sci Rep, 2014 Dec 18. PMID 25519916, Free PMC Article
    3. Parallel SCF adaptor capture proteomics reveals a role for SCFFBXL17 in NRF2 activation via BACH1 repressor turnover. Tan MK, et al. Mol Cell, 2013 Oct 10. PMID 24035498, Free PMC Article
    4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
    5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp761G122

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel regulator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein domain specific binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in central nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    hippocalcin-like protein 4

    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_001282396.2 → NP_001269325.1  hippocalcin-like protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001269325.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an additional exon in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL035404, AL136591, BC030827, BM669991, DA107675, DA220121
      Consensus CDS
      CCDS441.1
      UniProtKB/Swiss-Prot
      B2R5U2, D3DPU1, Q5TG97, Q8N611, Q9UM19
      UniProtKB/TrEMBL
      B4DG51
      Related
      ENSP00000481834.1, ENST00000617690.2
      Conserved Domains (1) summary
      COG5126
      Location:13 → 181
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    2. NM_001282397.2 → NP_001269326.1  hippocalcin-like protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001269326.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame coding exon, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AL035404, BM669991, DC333158
      Consensus CDS
      CCDS72761.1
      UniProtKB/TrEMBL
      B4DGW9
      Related
      ENSP00000484070.1, ENST00000612703.3
      Conserved Domains (1) summary
      COG5126
      Location:13 → 109
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    3. NM_016257.4 → NP_057341.1  hippocalcin-like protein 4 isoform 1

      See identical proteins and their annotated locations for NP_057341.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) and variant 2 encode the same isoform (1).
      Source sequence(s)
      AL035404, BC030827, BM669991
      Consensus CDS
      CCDS441.1
      UniProtKB/Swiss-Prot
      B2R5U2, D3DPU1, Q5TG97, Q8N611, Q9UM19
      UniProtKB/TrEMBL
      B4DG51
      Related
      ENSP00000361935.3, ENST00000372844.8
      Conserved Domains (1) summary
      COG5126
      Location:13 → 181
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      39678648..39691433 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      39548023..39560837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UM19.3 GenPept UniProtKB/Swiss-Prot:Q9UM19

    Gene LinkOut

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

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