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Aliases for HPCAL1 Gene

Aliases for HPCAL1 Gene

  • Hippocalcin Like 1 2 3 5
  • Calcium-Binding Protein BDR-1 2 3 4
  • Visinin-Like Protein 3 2 3 4
  • VILIP-3 3 4
  • HLP2 3 4
  • BDR1 3 4
  • Hippocalcin-Like Protein 1 3

External Ids for HPCAL1 Gene

Previous GeneCards Identifiers for HPCAL1 Gene

  • GC02P010228
  • GC02P010494
  • GC02P010464
  • GC02P010443

Summaries for HPCAL1 Gene

Entrez Gene Summary for HPCAL1 Gene

  • The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. It is highly similar to human hippocalcin protein and nearly identical to the rat and mouse hippocalcin like-1 proteins. It may be involved in the calcium-dependent regulation of rhodopsin phosphorylation and may be of relevance for neuronal signalling in the central nervous system. Several alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for HPCAL1 Gene

HPCAL1 (Hippocalcin Like 1) is a Protein Coding gene. Among its related pathways are Visual Cycle in Retinal Rods. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is HPCA.

UniProtKB/Swiss-Prot for HPCAL1 Gene

  • May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Gene Wiki entry for HPCAL1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPCAL1 Gene

Genomics for HPCAL1 Gene

Regulatory Elements for HPCAL1 Gene

Enhancers for HPCAL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F010403 0.9 FANTOM5 Ensembl ENCODE 56.9 +105.1 105136 8.3 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 YBX1 ZNF2 YY1 HPCAL1 LOC101929691 SNORA80B PIR41580
GH02F010327 0.8 FANTOM5 ENCODE 46.1 +27.8 27821 6.1 HDGF ATF1 PKNOX1 CREB3L1 ZFP64 SIN3A DMAP1 ZNF121 GATA2 ZNF263 HPCAL1 LOC101929691 SNORA80B TAF1B PIR41580
GH02F010399 1.2 FANTOM5 Ensembl ENCODE 25.1 +98.6 98561 3.6 ELF3 MLX ARID4B DMAP1 THRB ZNF48 RAD21 RARA FOS MIXL1 HPCAL1 LOC101929691 SNORA80B KLF11 PIR41580
GH02F010397 1.3 Ensembl ENCODE 22 +95.3 95330 2.0 FOSL1 KLF1 JUND POLR2A NRF1 MAX FOS HPCAL1 PIR41580
GH02F010374 1.4 FANTOM5 Ensembl ENCODE 21.6 +80.2 80212 16.6 PKNOX1 ARNT CREB3L1 ZFP64 SIN3A ZNF2 GATA2 ZNF207 FOS REST HPCAL1 LOC101929691 ENSG00000269973 PIR41580
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around HPCAL1 on UCSC Golden Path with GeneCards custom track

Promoters for HPCAL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000011312 1011 3401 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 CBX5 ZNF143 ZNF207

Genomic Location for HPCAL1 Gene

10,302,889 bp from pter
10,427,617 bp from pter
124,729 bases
Plus strand

Genomic View for HPCAL1 Gene

Genes around HPCAL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPCAL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPCAL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPCAL1 Gene

Proteins for HPCAL1 Gene

  • Protein details for HPCAL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hippocalcin-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q969S5

    Protein attributes for HPCAL1 Gene

    193 amino acids
    Molecular mass:
    22313 Da
    Quaternary structure:
    No Data Available
    • Probably binds two or three calcium ions.

neXtProt entry for HPCAL1 Gene

Post-translational modifications for HPCAL1 Gene

  • Ubiquitination at Lys 7
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HPCAL1 Gene

Domains & Families for HPCAL1 Gene

Gene Families for HPCAL1 Gene

Protein Domains for HPCAL1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 4 EF-hand domains.
  • Belongs to the recoverin family.
  • Contains 4 EF-hand domains.
  • Belongs to the recoverin family.
genes like me logo Genes that share domains with HPCAL1: view

Function for HPCAL1 Gene

Molecular function for HPCAL1 Gene

GENATLAS Biochemistry:
calcium binding protein,hippocalcin-like,expressed in brain
UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Gene Ontology (GO) - Molecular Function for HPCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HPCAL1: view
genes like me logo Genes that share phenotypes with HPCAL1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HPCAL1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HPCAL1 Gene

Localization for HPCAL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HPCAL1 Gene

Membrane; Lipid-anchor.

Subcellular locations from

Jensen Localization Image for HPCAL1 Gene COMPARTMENTS Subcellular localization image for HPCAL1 gene
Compartment Confidence
extracellular 5
cytosol 3
nucleus 2

Gene Ontology (GO) - Cellular Components for HPCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with HPCAL1: view

Pathways & Interactions for HPCAL1 Gene

SuperPathways for HPCAL1 Gene

SuperPathway Contained pathways
1 Visual Cycle in Retinal Rods
genes like me logo Genes that share pathways with HPCAL1: view

Pathways by source for HPCAL1 Gene

1 Qiagen pathway for HPCAL1 Gene

Gene Ontology (GO) - Biological Process for HPCAL1 Gene


No data available for SIGNOR curated interactions for HPCAL1 Gene

Drugs & Compounds for HPCAL1 Gene

(1) Drugs for HPCAL1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with HPCAL1: view

Transcripts for HPCAL1 Gene

Unigene Clusters for HPCAL1 Gene

Hippocalcin-like 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPCAL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d
SP1: - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - -
SP5: - - - - - -
SP6: - - - -
SP8: - - -
SP9: - -

Relevant External Links for HPCAL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HPCAL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HPCAL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HPCAL1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.0) and Brain - Cerebellum (x4.4).

Protein differential expression in normal tissues from HIPED for HPCAL1 Gene

This gene is overexpressed in Bone (21.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HPCAL1 Gene

Protein tissue co-expression partners for HPCAL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPCAL1 Gene:


SOURCE GeneReport for Unigene cluster for HPCAL1 Gene:

genes like me logo Genes that share expression patterns with HPCAL1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for HPCAL1 Gene

Orthologs for HPCAL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPCAL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HPCAL1 34 35
  • 99.31 (n)
(Monodelphis domestica)
Mammalia HPCAL1 35
  • 99 (a)
(Canis familiaris)
Mammalia HPCAL1 34 35
  • 94.13 (n)
(Bos Taurus)
Mammalia HPCAL1 34 35
  • 93.78 (n)
(Rattus norvegicus)
Mammalia Hpcal1 34
  • 92.4 (n)
(Mus musculus)
Mammalia Hpcal1 34 16 35
  • 92.06 (n)
(Ornithorhynchus anatinus)
Mammalia HPCAL1 35
  • 90 (a)
(Gallus gallus)
Aves HPCAL1 34 35
  • 87.74 (n)
(Anolis carolinensis)
Reptilia HPCAL1 35
  • 99 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hpcal1 34
  • 82.9 (n)
(Danio rerio)
Actinopterygii HPCAL1 35
  • 91 (a)
zgc:63695 34
  • 83.42 (n)
zgc73126 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007247 34
  • 76.72 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nca 36 34
  • 70.37 (n)
CG5744 36
  • 59 (a)
Frq 36
  • 58 (a)
CG7646 36
  • 47 (a)
(Caenorhabditis elegans)
Secernentea ncs-3 36
  • 55 (a)
ncs-2 36
  • 51 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 80 (a)
Species where no ortholog for HPCAL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HPCAL1 Gene

Gene Tree for HPCAL1 (if available)
Gene Tree for HPCAL1 (if available)

Paralogs for HPCAL1 Gene

Variants for HPCAL1 Gene

Sequence variations from dbSNP and Humsavar for HPCAL1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1003651 -- 10,327,951(+) TCATG(G/T)ATAAA intron-variant
rs1003652 -- 10,328,170(+) ATAGG(A/C)AGGTG intron-variant, upstream-variant-2KB
rs1003653 -- 10,329,390(+) aagga(A/G)cctgt intron-variant, upstream-variant-2KB
rs10167784 -- 10,330,162(+) GGCCT(C/T)TATGC intron-variant, upstream-variant-2KB
rs10169634 -- 10,395,229(+) CAGGT(C/T)TTGAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HPCAL1 Gene

Variant ID Type Subtype PubMed ID
dgv587e201 CNV deletion 23290073
dgv679e199 CNV deletion 23128226
esv1007136 CNV insertion 20482838
esv2719644 CNV deletion 23290073
esv2719646 CNV deletion 23290073
esv2719648 CNV deletion 23290073
esv2719650 CNV deletion 23290073
esv27364 CNV loss 19812545
esv3395574 CNV duplication 20981092
esv3446200 CNV insertion 20981092
esv3589797 CNV loss 21293372
esv3589798 CNV loss 21293372
nsv1007185 CNV gain 25217958
nsv1071973 CNV deletion 25765185
nsv1077349 CNV duplication 25765185
nsv2605 CNV insertion 18451855
nsv508827 CNV insertion 20534489

Variation tolerance for HPCAL1 Gene

Residual Variation Intolerance Score: 32.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.36; 7.94% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HPCAL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPCAL1 Gene

Disorders for HPCAL1 Gene

Relevant External Links for HPCAL1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HPCAL1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HPCAL1 Gene

Publications for HPCAL1 Gene

  1. Hypertension susceptibility genes on chromosome 2p24-p25 in a general Japanese population. (PMID: 15834280) Kamide K. … Miyata T. (J. Hypertens. 2005) 3 22 46 64
  2. Molecular cloning of a novel calcium-binding protein structurally related to hippocalcin from human brain and chromosomal mapping of its gene. (PMID: 8038222) Kobayashi M. … Noguchi T. (Biochim. Biophys. Acta 1994) 2 3 4 64
  3. Functional contribution of Ca2+ and Mg2+ to the intermolecular interaction of visinin-like proteins. (PMID: 16703469) Jheng F.F. … Chang L.S. (Protein J. 2006) 3 22 64
  4. Neuronal calcium sensor protein visinin-like protein-3 interacts with microsomal cytochrome b5 in a Ca2+-dependent manner. (PMID: 14739275) Oikawa K. … Tateno M. (J. Biol. Chem. 2004) 2 3 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for HPCAL1 Gene

Sources for HPCAL1 Gene

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