Human Gene NCS1 (ENST00000372398.6) from GENCODE V44
  Description: Homo sapiens neuronal calcium sensor 1 (NCS1), transcript variant 1, mRNA. (from RefSeq NM_014286)
RefSeq Summary (NM_014286): This gene is a member of the neuronal calcium sensor gene family, which encode calcium-binding proteins expressed predominantly in neurons. The protein encoded by this gene regulates G protein-coupled receptor phosphorylation in a calcium-dependent manner and can substitute for calmodulin. The protein is associated with secretory granules and modulates synaptic transmission and synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000372398.6
Gencode Gene: ENSG00000107130.10
Transcript (Including UTRs)
   Position: hg38 chr9:130,172,404-130,237,303 Size: 64,900 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr9:130,172,664-130,226,487 Size: 53,824 Coding Exon Count: 7 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:130,172,404-130,237,303)mRNA (may differ from genome)Protein (190 aa)
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-  Comments and Description Text from UniProtKB
  ID: NCS1_HUMAN
DESCRIPTION: RecName: Full=Neuronal calcium sensor 1; Short=NCS-1; AltName: Full=Frequenin homolog; AltName: Full=Frequenin-like protein; AltName: Full=Frequenin-like ubiquitous protein;
FUNCTION: Neuronal calcium sensor, regulator of G protein-coupled receptor phosphorylation in a calcium dependent manner. Directly regulates GRK1 (RHOK), but not GRK2 to GRK5. Can substitute for calmodulin (By similarity). Stimulates PI4KB kinase activity (By similarity). Involved in long-term synaptic plasticity through its interaction with PICK1 (By similarity). May also play a role in neuron differentiation through inhibition of the activity of N- type voltage-gated calcium channel (By similarity).
SUBUNIT: Interacts with KCND2. Interacts in a calcium-independent manner with PI4KB. This binding competes with CALN2/CABP7 binding to PI4KB (By similarity). Interacts with ARF1, ARF3, ARF5 and ARF6. Interacts in a calcium-dependent manner with PICK1 (via AH domain) (By similarity). Interacts with IL1RAPL1.
SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane; Peripheral membrane protein. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity). Cytoplasm, perinuclear region. Cell membrane; Peripheral membrane protein. Note=Associated with Golgi stacks. Post-synaptic densities of dendrites, and in the pre-synaptic nerve terminal at neuromuscular junctions.
MISCELLANEOUS: Binds 3 calcium ions via the second, third and fourth EF-hand.
SIMILARITY: Belongs to the recoverin family.
SIMILARITY: Contains 4 EF-hand domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NCS1
Diseases sorted by gene-association score: labyrinthitis (11), tracheitis (9), denture stomatitis (6), schizophrenia (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 224.11 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 2152.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -167.10260-0.643 Picture PostScript Text
3' UTR -1780.104331-0.411 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018248 - EF-hand
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR001125 - Recoverin

Pfam Domains:
PF00036 - EF hand

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1G8I - X-ray MuPIT 2LCP - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P62166
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
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Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0005245 voltage-gated calcium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0046872 metal ion binding

Biological Process:
GO:0010975 regulation of neuron projection development
GO:0045921 positive regulation of exocytosis
GO:0048015 phosphatidylinositol-mediated signaling
GO:0070588 calcium ion transmembrane transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0030425 dendrite
GO:0031045 dense core granule
GO:0031410 cytoplasmic vesicle
GO:0043231 intracellular membrane-bounded organelle
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC004856 - Homo sapiens frequenin homolog (Drosophila), mRNA (cDNA clone MGC:10261 IMAGE:3928335), complete cds.
JD191887 - Sequence 172911 from Patent EP1572962.
AF134479 - Homo sapiens neuronal calcium sensor mRNA, complete cds.
JD425756 - Sequence 406780 from Patent EP1572962.
AF186409 - Homo sapiens frequenin mRNA, complete cds.
X84048 - H.sapiens mRNA for frequenin-like ubiquitous protein.
JD458081 - Sequence 439105 from Patent EP1572962.
AB463656 - Synthetic construct DNA, clone: pF1KB6838, Homo sapiens FREQ gene for frequenin homolog, without stop codon, in Flexi system.
KJ898487 - Synthetic construct Homo sapiens clone ccsbBroadEn_07881 NCS1 gene, encodes complete protein.
JD025418 - Sequence 6442 from Patent EP1572962.
JD547274 - Sequence 528298 from Patent EP1572962.
JD158371 - Sequence 139395 from Patent EP1572962.
AL161981 - Homo sapiens mRNA; cDNA DKFZp761L1223 (from clone DKFZp761L1223).
JD114690 - Sequence 95714 from Patent EP1572962.
JD050523 - Sequence 31547 from Patent EP1572962.
JD125471 - Sequence 106495 from Patent EP1572962.
JD124882 - Sequence 105906 from Patent EP1572962.
JD464004 - Sequence 445028 from Patent EP1572962.
JD096573 - Sequence 77597 from Patent EP1572962.
JD315223 - Sequence 296247 from Patent EP1572962.
JD452960 - Sequence 433984 from Patent EP1572962.
JD076120 - Sequence 57144 from Patent EP1572962.
JD330584 - Sequence 311608 from Patent EP1572962.
JD221013 - Sequence 202037 from Patent EP1572962.
JD082537 - Sequence 63561 from Patent EP1572962.
AK023889 - Homo sapiens cDNA FLJ13827 fis, clone THYRO1000596.
JD559458 - Sequence 540482 from Patent EP1572962.
JD422924 - Sequence 403948 from Patent EP1572962.
JD547379 - Sequence 528403 from Patent EP1572962.
JD099760 - Sequence 80784 from Patent EP1572962.
JD313978 - Sequence 295002 from Patent EP1572962.
JD404930 - Sequence 385954 from Patent EP1572962.
JD454718 - Sequence 435742 from Patent EP1572962.
JD486310 - Sequence 467334 from Patent EP1572962.
JD294494 - Sequence 275518 from Patent EP1572962.
JD236507 - Sequence 217531 from Patent EP1572962.
JD212160 - Sequence 193184 from Patent EP1572962.
JD342810 - Sequence 323834 from Patent EP1572962.
JD115299 - Sequence 96323 from Patent EP1572962.
JD163376 - Sequence 144400 from Patent EP1572962.
JD513323 - Sequence 494347 from Patent EP1572962.
JD055796 - Sequence 36820 from Patent EP1572962.
JD184242 - Sequence 165266 from Patent EP1572962.
JD498442 - Sequence 479466 from Patent EP1572962.
JD398874 - Sequence 379898 from Patent EP1572962.
JD386266 - Sequence 367290 from Patent EP1572962.
JD251602 - Sequence 232626 from Patent EP1572962.
JD235627 - Sequence 216651 from Patent EP1572962.
JD273616 - Sequence 254640 from Patent EP1572962.
JD543765 - Sequence 524789 from Patent EP1572962.
JD424249 - Sequence 405273 from Patent EP1572962.
JD233250 - Sequence 214274 from Patent EP1572962.
JD451116 - Sequence 432140 from Patent EP1572962.
JD221518 - Sequence 202542 from Patent EP1572962.
JD343762 - Sequence 324786 from Patent EP1572962.
JD292669 - Sequence 273693 from Patent EP1572962.
AK024709 - Homo sapiens cDNA: FLJ21056 fis, clone CAS00684.
JD417252 - Sequence 398276 from Patent EP1572962.
JD188656 - Sequence 169680 from Patent EP1572962.
JD190565 - Sequence 171589 from Patent EP1572962.
JD492809 - Sequence 473833 from Patent EP1572962.
JD269984 - Sequence 251008 from Patent EP1572962.
JD276627 - Sequence 257651 from Patent EP1572962.
JD202287 - Sequence 183311 from Patent EP1572962.
BC008698 - Homo sapiens, clone IMAGE:2822393, mRNA.
JD446183 - Sequence 427207 from Patent EP1572962.
JD511215 - Sequence 492239 from Patent EP1572962.
JD519033 - Sequence 500057 from Patent EP1572962.
JD215149 - Sequence 196173 from Patent EP1572962.
JD353294 - Sequence 334318 from Patent EP1572962.
JD398530 - Sequence 379554 from Patent EP1572962.
JD254267 - Sequence 235291 from Patent EP1572962.
JD418401 - Sequence 399425 from Patent EP1572962.
JD477199 - Sequence 458223 from Patent EP1572962.
JD458214 - Sequence 439238 from Patent EP1572962.
JD104682 - Sequence 85706 from Patent EP1572962.
JD407771 - Sequence 388795 from Patent EP1572962.
JD535142 - Sequence 516166 from Patent EP1572962.
JD484619 - Sequence 465643 from Patent EP1572962.
JD142841 - Sequence 123865 from Patent EP1572962.
JD052468 - Sequence 33492 from Patent EP1572962.
JD336118 - Sequence 317142 from Patent EP1572962.
JD069688 - Sequence 50712 from Patent EP1572962.
JD365828 - Sequence 346852 from Patent EP1572962.
JD387701 - Sequence 368725 from Patent EP1572962.
JD117419 - Sequence 98443 from Patent EP1572962.
JD336614 - Sequence 317638 from Patent EP1572962.
JD444071 - Sequence 425095 from Patent EP1572962.
JD472822 - Sequence 453846 from Patent EP1572962.
JD472823 - Sequence 453847 from Patent EP1572962.
JD540645 - Sequence 521669 from Patent EP1572962.
JD470828 - Sequence 451852 from Patent EP1572962.
JD444014 - Sequence 425038 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000372398.1, ENST00000372398.2, ENST00000372398.3, ENST00000372398.4, ENST00000372398.5, FLUP, FREQ, NCS1_HUMAN, NM_014286, P36610, P62166, Q9UK26, uc004bzi.1, uc004bzi.2, uc004bzi.3
UCSC ID: ENST00000372398.6
RefSeq Accession: NM_014286
Protein: P62166 (aka NCS1_HUMAN)
CCDS: CCDS6932.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.