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HPCAL4 Gene(Protein Coding)

Hippocalcin Like 4

GCID:
GC01M039678
GIFtS:
54
Genes Participants
UDN Logo

Aliases for HPCAL4 Gene

Aliases for HPCAL4 Gene

  • Hippocalcin Like 4 2 3 5
  • HLP4 3 4
  • Hippocalcin-Like Protein 4 3

External Ids for HPCAL4 Gene

Previous GeneCards Identifiers for HPCAL4 Gene

  • GC01M040174
  • GC01M039148
  • GC01M039608
  • GC01M039557
  • GC01M039813
  • GC01M039916
  • GC01M038263

Summaries for HPCAL4 Gene

Entrez Gene Summary for HPCAL4 Gene

  • 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]

GeneCards Summary for HPCAL4 Gene

HPCAL4 (Hippocalcin Like 4) is a Protein Coding gene. Diseases associated with HPCAL4 include Holoprosencephaly-3. Among its related pathways are Visual Cycle in Retinal Rods. GO annotations related to this gene include calcium ion binding and protein C-terminus binding. An important paralog of this gene is VSNL1.

UniProtKB/Swiss-Prot for HPCAL4 Gene

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

Gene Wiki entry for HPCAL4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPCAL4 Gene

Genomics for HPCAL4 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HPCAL4 Gene

Enhancers for HPCAL4 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
GH01G039645 1.3 Ensembl ENCODE dbSUPER 24.3 +44.8 44803 3.4 BCOR CTCF TEAD4 MAX ZMYM3 TCF12 ZFHX2 POLR2A EGR1 SCRT2 HPCAL4 NT5C1A PPIE PABPC4 HEYL OXCT2
GH01G039652 1 ENCODE dbSUPER 24 +38.9 38877 1.4 CTCF ESRRA RB1 ETV1 ZNF384 ZNF2 RAD21 ZEB1 ZNF664 ZFHX2 HPCAL4 PPIE PABPC4 HEYL NT5C1A
GH01G039690 1.1 Ensembl ENCODE 19.3 0.0 -42 1.8 PKNOX1 ZSCAN4 INSM2 KLF17 BMI1 ZNF2 FOS SP3 MIER1 NFYC HPCAL4 PPIE
GH01G039631 1.5 Ensembl ENCODE dbSUPER 11.5 +58.7 58724 2.4 HDGF ATF1 PKNOX1 SIN3A SLC30A9 GLIS2 GATA2 ELK1 ZNF143 KLF7 ENSG00000225903 HPCAL4 OXCT2 GC01M039576
GH01G039653 1.3 Ensembl ENCODE dbSUPER 11.2 +37.9 37895 0.4 RB1 ZNF2 RAD21 ZEB1 GATA2 ZNF143 CREM EGR2 ZNF654 CEBPB ENSG00000225903 HPCAL4 PPIE PABPC4 HEYL NT5C1A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HPCAL4 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HPCAL4 gene promoter:

Genomic Location for HPCAL4 Gene

Chromosome:
1
Start:
39,678,648 bp from pter
End:
39,691,710 bp from pter
Size:
13,063 bases
Orientation:
Minus strand

Genomic View for HPCAL4 Gene

Genes around HPCAL4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPCAL4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPCAL4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HPCAL4 Gene

Proteins for HPCAL4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HPCAL4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UM19-HPCL4_HUMAN
    Recommended name:
    Hippocalcin-like protein 4
    Protein Accession:
    Q9UM19
    Secondary Accessions:
    • B2R5U2
    • D3DPU1
    • Q5TG97
    • Q8N611

    Protein attributes for HPCAL4 Gene

    Size:
    191 amino acids
    Molecular mass:
    22202 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Probably binds two or three calcium ions.

neXtProt entry for HPCAL4 Gene

Protein Expression for HPCAL4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HPCAL4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HPCAL4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HPCAL4 Gene

Domains & Families for HPCAL4 Gene

Gene Families for HPCAL4 Gene

HGNC:

Protein Domains for HPCAL4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HPCAL4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UM19

UniProtKB/Swiss-Prot:

HPCL4_HUMAN :
  • Belongs to the recoverin family.
Family:
  • Belongs to the recoverin family.
genes like me logo Genes that share domains with HPCAL4: view

Function for HPCAL4 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HPCAL4 Gene

UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Gene Ontology (GO) - Molecular Function for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005246 calcium channel regulator activity IEA --
GO:0005509 calcium ion binding IEA,TAS --
GO:0005515 protein binding IPI 16189514
GO:0008022 protein C-terminus binding IEA --
GO:0019904 protein domain specific binding IEA --
genes like me logo Genes that share ontologies with HPCAL4: view

Phenotypes for HPCAL4 Gene

MGI mutant phenotypes for HPCAL4:
inferred from 1 alleles
GenomeRNAi human phenotypes for HPCAL4:
genes like me logo Genes that share phenotypes with HPCAL4: view

Animal Models for HPCAL4 Gene

MGI Knock Outs for HPCAL4:

Animal Model Products

CRISPR Products

miRNA for HPCAL4 Gene

miRTarBase miRNAs that target HPCAL4

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HPCAL4 Gene

Localization for HPCAL4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HPCAL4 gene
Compartment Confidence
cytosol 3
peroxisome 2
extracellular 1
nucleus 1

Gene Ontology (GO) - Cellular Components for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
genes like me logo Genes that share ontologies with HPCAL4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HPCAL4 Gene

Pathways & Interactions for HPCAL4 Gene

SuperPathways for HPCAL4 Gene

PathCards logo More details on SuperPathways for HPCAL4
SuperPathway Contained pathways
1 Visual Cycle in Retinal Rods
Visual Cycle in Retinal Rods
-
genes like me logo Genes that share pathways with HPCAL4: view

Pathways by source for HPCAL4 Gene

1 Qiagen pathway for HPCAL4 Gene

Gene Ontology (GO) - Biological Process for HPCAL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007417 central nervous system development TAS 10520747
GO:0065009 regulation of molecular function IEA --
genes like me logo Genes that share ontologies with HPCAL4: view

No data available for SIGNOR curated interactions for HPCAL4 Gene

Drugs & Compounds for HPCAL4 Gene

Products:

  1. Drug

(1) Drugs for HPCAL4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with HPCAL4: view

Transcripts for HPCAL4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HPCAL4 Gene

(4) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(81) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HPCAL4 Gene

Hippocalcin like 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPCAL4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b
SP1: - -
SP2: -
SP3: - - -
SP4: -

Relevant External Links for HPCAL4 Gene

GeneLoc Exon Structure for
HPCAL4
ECgene alternative splicing isoforms for
HPCAL4

Expression for HPCAL4 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPCAL4 Gene

mRNA expression in normal human tissues for HPCAL4 Gene
mRNA expression by BioGPS for HPCAL4 GenemRNA expression by GTEx for HPCAL4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HPCAL4 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x6.4), Brain - Cortex (x6.2), Brain - Amygdala (x5.8), Brain - Frontal Cortex (BA9) (x5.3), Brain - Nucleus accumbens (basal ganglia) (x5.1), Brain - Hippocampus (x4.5), Brain - Cerebellum (x4.2), and Brain - Cerebellar Hemisphere (x4.1).

Protein differential expression in normal tissues from HIPED for HPCAL4 Gene

This gene is overexpressed in Brain (34.6) and Frontal cortex (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HPCAL4 Gene



Protein tissue co-expression partners for HPCAL4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPCAL4 Gene:

HPCAL4

SOURCE GeneReport for Unigene cluster for HPCAL4 Gene:

Hs.743975

Evidence on tissue expression from TISSUES for HPCAL4 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with HPCAL4: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HPCAL4 Gene

Orthologs for HPCAL4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPCAL4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HPCAL4 34 35
  • 100 (n)
dog
(Canis familiaris)
 Mammalia HPCAL4 34 35
  • 95.46 (n)
cow
(Bos Taurus)
 Mammalia HPCAL4 34 35
  • 94.59 (n)
mouse
(Mus musculus)
 Mammalia Hpcal4 34 16 35
  • 93.37 (n)
rat
(Rattus norvegicus)
 Mammalia Hpcal4 34
  • 92.5 (n)
oppossum
(Monodelphis domestica)
 Mammalia HPCAL4 35
  • 89 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HPCAL4 34 35
  • 87.09 (n)
lizard
(Anolis carolinensis)
 Reptilia HPCAL4 35
  • 94 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hpcal4 34
  • 78.53 (n)
zebrafish
(Danio rerio)
 Actinopterygii hpcal4 34 35
  • 79.41 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Nca 36 35
  • 71 (a)
CG7646 36
  • 43 (a)
worm
(Caenorhabditis elegans)
 Secernentea ncs-2 36
  • 46 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 64 (a)
 OneToMany
Species where no ortholog for HPCAL4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 HPCAL4 Gene

ENSEMBL:
Gene Tree for HPCAL4 (if available)
TreeFam:
Gene Tree for HPCAL4 (if available)

Paralogs for HPCAL4 Gene

Paralogs for HPCAL4 Gene

(18) SIMAP similar genes for HPCAL4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HPCAL4: view

Variants for HPCAL4 Gene

Sequence variations from dbSNP and Humsavar for HPCAL4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000025305 -- 39,680,422(+) TTCTG(C/T)GTGGT utr-variant-3-prime
rs1000070459 -- 39,688,016(+) AAACT(A/G)GCTCA intron-variant
rs1000215259 -- 39,686,613(+) GAAGT(A/G)TTGTT intron-variant
rs1000218072 -- 39,692,663(+) TCAGA(C/T)CTGCC upstream-variant-2KB
rs1000270321 -- 39,692,982(+) CTTGG(A/G)GACCC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HPCAL4 Gene

Variant ID Type Subtype PubMed ID
nsv1116447 OTHER inversion 24896259
nsv546062 CNV gain 21841781
nsv7177 OTHER inversion 18451855

Variation tolerance for HPCAL4 Gene

Residual Variation Intolerance Score: 36.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.19; 4.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HPCAL4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HPCAL4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPCAL4 Gene

Disorders for HPCAL4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HPCAL4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
holoprosencephaly-3
  • holoprosencephaly 3
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for HPCAL4

Genetic Association Database (GAD)
HPCAL4
Human Genome Epidemiology (HuGE) Navigator
HPCAL4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HPCAL4
genes like me logo Genes that share disorders with HPCAL4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HPCAL4 Gene

Publications for HPCAL4 Gene

  1. Isolation of two human cDNAs, HLP3 and HLP4, homologous to the neuron-specific calcium-binding protein genes. (PMID: 10520747) Kobayashi M. … Takamatsu K. (DNA Seq. 1998) 2 3 4 22 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  4. 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
  5. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S. … Poustka A. (Genome Res. 2001) 3 4 64

Products for HPCAL4 Gene

Sources for HPCAL4 Gene

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