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NCALD neurocalcin delta [ Homo sapiens (human) ]

Gene ID: 83988, updated on 21-Jun-2020

Summary

Official Symbol
NCALDprovided by HGNC
Official Full Name
neurocalcin deltaprovided by HGNC
Primary source
HGNC:HGNC:7655
See related
Ensembl:ENSG00000104490 MIM:606722
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
Summary
This gene encodes a member of the neuronal calcium sensor (NCS) family of calcium-binding proteins. The protein contains an N-terminal myristoylation signal and four EF-hand calcium binding loops. The protein is cytosolic at resting calcium levels; however, elevated intracellular calcium levels induce a conformational change that exposes the myristoyl group, resulting in protein association with membranes and partial co-localization with the perinuclear trans-golgi network. The protein is thought to be a regulator of G protein-coupled receptor signal transduction. Several alternatively spliced variants of this gene have been determined, all of which encode the same protein; additional variants may exist but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 22.6), salivary gland (RPKM 11.3) and 20 other tissues See more
Orthologs

Genomic context

See NCALD in Genome Data Viewer
Location:
8q22.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (101686542..102125081, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (102698770..103137135, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene grainyhead like transcription factor 2 Neighboring gene probable ribosome biogenesis protein RLP24 pseudogene Neighboring gene PDCL3 pseudogene 2 Neighboring gene uncharacterized LOC107986963 Neighboring gene uncharacterized LOC104054148 Neighboring gene 6.8 kDa mitochondrial proteolipid-like Neighboring gene microRNA 5680

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?

Phenotypes

NHGRI GWAS Catalog

Description
Common genetic variation and performance on standardized cognitive tests.
NHGRI GWA Catalog
Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
NHGRI GWA Catalog
Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC33870, MGC74858

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding IDA
Inferred from Direct Assay
more info
PubMed 
alpha-tubulin binding IEA
Inferred from Electronic Annotation
more info
 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
clathrin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
tubulin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
calcium-mediated signaling IEA
Inferred from Electronic Annotation
more info
 
regulation of systemic arterial blood pressure IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
clathrin coat of trans-Golgi network vesicle NAS
Non-traceable Author Statement
more info
PubMed 
cytosol NAS
Non-traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
intracellular IDA
Inferred from Direct Assay
more info
 

NCBI Reference Sequences (RefSeq)

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_001040624.1NP_001035714.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035714.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes five untranslated exons at the 5' end.
    Source sequence(s)
    AK096515, AP000426, BC063428, BM681731, DA417037
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  2. NM_001040625.1NP_001035715.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035715.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC063428, BM681731, DA417037
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Related
    ENSP00000428105.1, ENST00000521599.5
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  3. NM_001040626.1NP_001035716.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035716.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC063428, BM681731, DA185335, DA417037
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Related
    ENSP00000310587.3, ENST00000311028.4
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  4. NM_001040627.1NP_001035717.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035717.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two exons in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC036098, BC063428, BM681731, DA417037
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  5. NM_001040628.1NP_001035718.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035718.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC063428, BM681731, DA417037, DA776593
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  6. NM_001040629.1NP_001035719.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035719.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC063428, BM681731, DA417037, DA779293
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  7. NM_001040630.1NP_001035720.1  neurocalcin-delta

    See identical proteins and their annotated locations for NP_001035720.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1.
    Source sequence(s)
    AP000426, BC063428, BM681731, DA215759, DB284042
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Related
    ENSP00000379256.1, ENST00000395923.5
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  8. NM_032041.3NP_114430.2  neurocalcin-delta

    See identical proteins and their annotated locations for NP_114430.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1.
    Source sequence(s)
    AL136612, AP000426, BC063428, BM681731, DA211806
    Consensus CDS
    CCDS6292.1
    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Related
    ENSP00000220931.6, ENST00000220931.11
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    101686542..102125081 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447296.1XP_024303064.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  2. XM_024447297.1XP_024303065.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  3. XM_017013901.1XP_016869390.1  neurocalcin-delta isoform X2

    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  4. XM_024447301.1XP_024303069.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  5. XM_024447299.1XP_024303067.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  6. XM_011517333.2XP_011515635.1  neurocalcin-delta isoform X2

    See identical proteins and their annotated locations for XP_011515635.1

    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  7. XM_024447298.1XP_024303066.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  8. XM_024447300.1XP_024303068.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  9. XM_024447304.1XP_024303072.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  10. XM_011517335.2XP_011515637.1  neurocalcin-delta isoform X2

    See identical proteins and their annotated locations for XP_011515637.1

    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  11. XM_011517334.2XP_011515636.1  neurocalcin-delta isoform X2

    See identical proteins and their annotated locations for XP_011515636.1

    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  12. XM_024447303.1XP_024303071.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  13. XM_011517332.3XP_011515634.1  neurocalcin-delta isoform X2

    See identical proteins and their annotated locations for XP_011515634.1

    UniProtKB/Swiss-Prot
    P61601
    UniProtKB/TrEMBL
    B2RB70
    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  14. XM_024447302.1XP_024303070.1  neurocalcin-delta isoform X2

    Conserved Domains (1) summary
    COG5126
    Location:14179
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
  15. XM_017013900.1XP_016869389.1  neurocalcin-delta isoform X1

RNA

  1. XR_001745607.1 RNA Sequence

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