Human Gene NCALD (ENST00000220931.11_7) from GENCODE V47lift37
  Description: neurocalcin delta, transcript variant 8 (from RefSeq NM_032041.3)
Gencode Transcript: ENST00000220931.11_7
Gencode Gene: ENSG00000104490.18_13
Transcript (Including UTRs)
   Position: hg19 chr8:102,698,770-102,803,197 Size: 104,428 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr8:102,701,537-102,731,857 Size: 30,321 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:102,698,770-102,803,197)mRNA (may differ from genome)Protein (193 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NCALD_HUMAN
DESCRIPTION: RecName: Full=Neurocalcin-delta;
FUNCTION: May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.
TISSUE SPECIFICITY: Retina, cerebrum, cerebellum, brain stem, spinal cord, testis, ovary and small intestine.
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 45.00 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 318.54 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 -37.10127-0.292 Picture PostScript Text
3' UTR -825.502767-0.298 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
PF13202 - EF hand
PF13405 - EF-hand domain
PF13499 - EF-hand domain pair
PF13833 - EF-hand domain pair

SCOP Domains:
63446 - Type I dockerin domain
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on P61601
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0015276 ligand-gated ion channel activity
GO:0015631 tubulin binding
GO:0030276 clathrin binding
GO:0043014 alpha-tubulin binding
GO:0046872 metal ion binding

Biological Process:
GO:0003073 regulation of systemic arterial blood pressure
GO:0016192 vesicle-mediated transport
GO:0019722 calcium-mediated signaling
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0005622 intracellular
GO:0005829 cytosol
GO:0030130 clathrin coat of trans-Golgi network vesicle


-  Descriptions from all associated GenBank mRNAs
  AK096515 - Homo sapiens cDNA FLJ39196 fis, clone OCBBF2005066, highly similar to NEUROCALCIN DELTA.
AB209015 - Homo sapiens mRNA for Neurocalcin delta variant protein.
AL136612 - Homo sapiens mRNA; cDNA DKFZp564B2123 (from clone DKFZp564B2123).
BC036098 - Homo sapiens neurocalcin delta, mRNA (cDNA clone MGC:33870 IMAGE:5274150), complete cds.
AF251061 - Homo sapiens neurocalcin mRNA, complete cds.
AK055073 - Homo sapiens cDNA FLJ30511 fis, clone BRAWH2000636, highly similar to NEUROCALCIN DELTA.
BC063428 - Homo sapiens neurocalcin delta, mRNA (cDNA clone MGC:74858 IMAGE:5240958), complete cds.
AK314523 - Homo sapiens cDNA, FLJ95342, highly similar to Homo sapiens neurocalcin delta (NCALD), mRNA.
BC009949 - Homo sapiens neurocalcin delta, mRNA (cDNA clone IMAGE:4298903), partial cds.
AF052142 - Homo sapiens clone 24665 mRNA sequence.
JD244106 - Sequence 225130 from Patent EP1572962.
JD101415 - Sequence 82439 from Patent EP1572962.
JD085660 - Sequence 66684 from Patent EP1572962.
JD547480 - Sequence 528504 from Patent EP1572962.
JD539185 - Sequence 520209 from Patent EP1572962.
JD526177 - Sequence 507201 from Patent EP1572962.
JD037064 - Sequence 18088 from Patent EP1572962.
JD050456 - Sequence 31480 from Patent EP1572962.
JD063689 - Sequence 44713 from Patent EP1572962.
JD410624 - Sequence 391648 from Patent EP1572962.
JD224343 - Sequence 205367 from Patent EP1572962.
JD315302 - Sequence 296326 from Patent EP1572962.
JD273135 - Sequence 254159 from Patent EP1572962.
JD116727 - Sequence 97751 from Patent EP1572962.
JD269493 - Sequence 250517 from Patent EP1572962.
JD362521 - Sequence 343545 from Patent EP1572962.
JD438066 - Sequence 419090 from Patent EP1572962.
JD120142 - Sequence 101166 from Patent EP1572962.
JD392769 - Sequence 373793 from Patent EP1572962.
JD281881 - Sequence 262905 from Patent EP1572962.
JD303616 - Sequence 284640 from Patent EP1572962.
JD475793 - Sequence 456817 from Patent EP1572962.
JD067543 - Sequence 48567 from Patent EP1572962.
JD437523 - Sequence 418547 from Patent EP1572962.
JD068832 - Sequence 49856 from Patent EP1572962.
JD066087 - Sequence 47111 from Patent EP1572962.
JD048925 - Sequence 29949 from Patent EP1572962.
JD350035 - Sequence 331059 from Patent EP1572962.
JD162052 - Sequence 143076 from Patent EP1572962.
JD146641 - Sequence 127665 from Patent EP1572962.
AK055097 - Homo sapiens cDNA FLJ30535 fis, clone BRAWH2001159, moderately similar to NEUROCALCIN DELTA.
JD293889 - Sequence 274913 from Patent EP1572962.
JD284024 - Sequence 265048 from Patent EP1572962.
JD091218 - Sequence 72242 from Patent EP1572962.
JD386604 - Sequence 367628 from Patent EP1572962.
JD133240 - Sequence 114264 from Patent EP1572962.
JD168620 - Sequence 149644 from Patent EP1572962.
JD533999 - Sequence 515023 from Patent EP1572962.
JD489969 - Sequence 470993 from Patent EP1572962.
JD562387 - Sequence 543411 from Patent EP1572962.
JD166113 - Sequence 147137 from Patent EP1572962.
JD280576 - Sequence 261600 from Patent EP1572962.
CU687710 - Synthetic construct Homo sapiens gateway clone IMAGE:100021593 5' read NCALD mRNA.
KJ894919 - Synthetic construct Homo sapiens clone ccsbBroadEn_04313 NCALD gene, encodes complete protein.
KJ899748 - Synthetic construct Homo sapiens clone ccsbBroadEn_09142 NCALD gene, encodes complete protein.
EU446538 - Synthetic construct Homo sapiens clone IMAGE:100070049; IMAGE:100011747; FLH258254.01L neurocalcin delta (NCALD) gene, encodes complete protein.
AB528192 - Synthetic construct DNA, clone: pF1KE0169, Homo sapiens NCALD gene for neurocalcin delta, without stop codon, in Flexi system.
AM392680 - Synthetic construct Homo sapiens clone DKFZp564B2123.1E5 for hypothetical protein (NCALD gene).
AM393346 - Synthetic construct Homo sapiens clone IMAGE:100002130 for hypothetical protein (NCALD gene).
JD272646 - Sequence 253670 from Patent EP1572962.
JD440819 - Sequence 421843 from Patent EP1572962.
JD483930 - Sequence 464954 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P61601 (Reactome details) participates in the following event(s):

R-HSA-451283 kainate receptor binds glutamate
R-HSA-451311 Activation of Ca-permeable Kainate receptors
R-HSA-451308 Activation of Ca-permeable Kainate Receptor
R-HSA-451306 Ionotropic activity of kainate receptors
R-HSA-451326 Activation of kainate receptors upon glutamate binding
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000220931.1, ENST00000220931.10, ENST00000220931.2, ENST00000220931.3, ENST00000220931.4, ENST00000220931.5, ENST00000220931.6, ENST00000220931.7, ENST00000220931.8, ENST00000220931.9, NCALD_HUMAN, NM_032041, P29554, P61601, Q8IYC3, Q9H0W2, uc317czz.1, uc317czz.2
UCSC ID: ENST00000220931.11_7
RefSeq Accession: NM_032041.3
Protein: P61601 (aka NCALD_HUMAN or NCAD_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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