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    HPCAL1 hippocalcin like 1 [ Homo sapiens (human) ]

    Gene ID: 3241, updated on 10-Dec-2024

    Summary

    Official Symbol
    HPCAL1provided by HGNC
    Official Full Name
    hippocalcin like 1provided by HGNC
    Primary source
    HGNC:HGNC:5145
    See related
    Ensembl:ENSG00000115756 MIM:600207; AllianceGenome:HGNC:5145
    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
    BDR1; HLP2; VILIP-3
    Summary
    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]
    Expression
    Ubiquitous expression in lung (RPKM 11.7), small intestine (RPKM 9.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HPCAL1 in Genome Data Viewer
    Location:
    2p25.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10302904..10427604)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10330643..10457210)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10443030..10567730)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:10422935-10424134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10424193-10424793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10425933-10426432 Neighboring gene uncharacterized LOC101929691 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10429268-10430467 Neighboring gene RNA, 7SL, cytoplasmic 66, pseudogene Neighboring gene small nucleolar RNA SNORA51 Neighboring gene CRISPRi-validated cis-regulatory element chr2.403 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10443229-10443426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11161 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10459734-10460234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10460235-10460735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10471739-10472326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10484271-10484771 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr2:10508004-10508811 Neighboring gene Sharpr-MPRA regulatory region 2000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10513139-10513866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10513867-10514592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10522419-10523074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10523075-10523728 Neighboring gene uncharacterized LOC124905972 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10547784-10548983 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559385-10559972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559973-10560560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10564889-10565701 Neighboring gene uncharacterized LOC124907732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10572745-10573710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10573711-10574675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15303 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10586390-10586619 Neighboring gene small nucleolar RNA, H/ACA box 80B Neighboring gene ornithine decarboxylase 1

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    hippocalcin-like protein 1
    Names
    calcium-binding protein BDR-1
    visinin-like protein 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001258357.2NP_001245286.1  hippocalcin-like protein 1

      See identical proteins and their annotated locations for NP_001245286.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC007249, AF070616, BC017482, BU145561
      Consensus CDS
      CCDS1671.1
      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Related
      ENSP00000482993.1, ENST00000622018.4
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    2. NM_001258358.2NP_001245287.1  hippocalcin-like protein 1

      See identical proteins and their annotated locations for NP_001245287.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC007249, AF070616, BC017482, BI601950
      Consensus CDS
      CCDS1671.1
      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Related
      ENSP00000478231.1, ENST00000613496.4
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    3. NM_001258359.2NP_001245288.1  hippocalcin-like protein 1

      See identical proteins and their annotated locations for NP_001245288.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents the longest transcript. All five variants encode the same protein.
      Source sequence(s)
      AC007249, AF070616, AK292280, BC017482
      Consensus CDS
      CCDS1671.1
      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Related
      ENSP00000483786.1, ENST00000620771.4
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    4. NM_002149.4NP_002140.2  hippocalcin-like protein 1

      See identical proteins and their annotated locations for NP_002140.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC007249, AF070616, BC017482, BI603158
      Consensus CDS
      CCDS1671.1
      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Related
      ENSP00000310749.3, ENST00000307845.8
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    5. NM_134421.3NP_602293.1  hippocalcin-like protein 1

      See identical proteins and their annotated locations for NP_602293.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC007240, AC007249, AF070616, AK000596
      Consensus CDS
      CCDS1671.1
      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Related
      ENSP00000371184.3, ENST00000381765.7
      Conserved Domains (1) summary
      COG5126
      Location:13179
      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      10302904..10427604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444095.1XP_047300051.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    2. XM_047444099.1XP_047300055.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    3. XM_005246163.2XP_005246220.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005246220.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    4. XM_005246160.2XP_005246217.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005246217.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    5. XM_011510347.2XP_011508649.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011508649.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    6. XM_005246162.2XP_005246219.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005246219.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    7. XM_005246161.2XP_005246218.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005246218.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    8. XM_011510349.3XP_011508651.1  hippocalcin-like protein 1 isoform X2

      See identical proteins and their annotated locations for XP_011508651.1

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
      Conserved Domains (1) summary
      COG5126
      Location:13161
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    9. XM_047444101.1XP_047300057.1  hippocalcin-like protein 1 isoform X2

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
    10. XM_047444097.1XP_047300053.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    11. XM_011510348.2XP_011508650.1  hippocalcin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011508650.1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    12. XM_047444096.1XP_047300052.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    13. XM_017003953.3XP_016859442.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
      Conserved Domains (1) summary
      COG5126
      Location:13179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    14. XM_047444100.1XP_047300056.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1

    RNA

    1. XR_007073115.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      10330643..10457210
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341664.1XP_054197639.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    2. XM_054341672.1XP_054197647.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    3. XM_054341661.1XP_054197636.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    4. XM_054341673.1XP_054197648.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    5. XM_054341668.1XP_054197643.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    6. XM_054341660.1XP_054197635.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    7. XM_054341666.1XP_054197641.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    8. XM_054341667.1XP_054197642.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    9. XM_054341665.1XP_054197640.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    10. XM_054341680.1XP_054197655.1  hippocalcin-like protein 1 isoform X2

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
    11. XM_054341677.1XP_054197652.1  hippocalcin-like protein 1 isoform X2

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
    12. XM_054341676.1XP_054197651.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    13. XM_054341662.1XP_054197637.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    14. XM_054341670.1XP_054197645.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    15. XM_054341674.1XP_054197649.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    16. XM_054341669.1XP_054197644.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    17. XM_054341679.1XP_054197654.1  hippocalcin-like protein 1 isoform X2

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
    18. XM_054341663.1XP_054197638.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    19. XM_054341671.1XP_054197646.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1
    20. XM_054341678.1XP_054197653.1  hippocalcin-like protein 1 isoform X2

      UniProtKB/TrEMBL
      E9PC71, Q68CP5
    21. XM_054341675.1XP_054197650.1  hippocalcin-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P37235, Q969S5
      UniProtKB/TrEMBL
      D6W4Z9, Q5U068, Q6FGY1

    RNA

    1. XR_008486354.1 RNA Sequence