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HPCAL1 hippocalcin like 1 [ Homo sapiens (human) ]

Gene ID: 3241, updated on 12-Aug-2022

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
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Genomic context

See HPCAL1 in Genome Data Viewer
Location:
2p25.1
Exon count:
15
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10302904..10427604)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10331479..10457205)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10443030..10567730)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929691 Neighboring gene small nucleolar RNA SNORA51 Neighboring gene CRISPRi-validated cis-regulatory element chr2.403 Neighboring gene Sharpr-MPRA regulatory region 2000 Neighboring gene uncharacterized LOC124905972 Neighboring gene uncharacterized LOC124907732 Neighboring gene small nucleolar RNA, H/ACA box 80B Neighboring gene ornithine decarboxylase 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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, O75544, 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, O75544, 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, O75544, 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, O75544, 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, O75544, 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    Q969S5
    UniProtKB/TrEMBL
    D6W4Z9
  2. XM_047444099.1XP_047300055.1  hippocalcin-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q969S5
    UniProtKB/TrEMBL
    D6W4Z9
  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, 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, 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, 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, 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, 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

    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

  10. XM_047444097.1XP_047300053.1  hippocalcin-like protein 1 isoform X1

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

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

RNA

  1. XR_007073115.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    10331479..10457205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)