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HPCAL4 hippocalcin like 4 [ Homo sapiens (human) ]

Gene ID: 51440, updated on 2-Nov-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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39678648..39691433, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39548023..39560837, complement)
RS_2024_09 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 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 
involved_in regulation of signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  

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_2024_08

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

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