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CALM3
HPA
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Brain region
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Tau score
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Interacting gene (ensg_id)
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ipTM
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  • SUMMARY

  • TISSUE

  • BRAIN

  • SINGLE CELL

  • SUBCELL

  • CANCER

  • BLOOD

  • CELL LINE

  • STRUCTURE

  • INTERACTION

  • CALM3
INTERACTION INTERACTION METABOLIC PATHWAYS Show tissue menu
ISOLATED
Protein interactions
Protein interactions
Methods
Human metabolism
Metabolic proteins
Methods
GENERAL INFORMATIONi

General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.

Gene namei

Official gene symbol, which is typically a short form of the gene name, according to HGNC.

CALM3
Synonyms PHKD, PHKD3
Gene descriptioni

Full gene name according to HGNC.

Calmodulin 3
Protein classi

Assigned HPA protein class(es) for the encoded protein(s).

Read more
Disease related genes
Human disease related genes
Metabolic proteins
RAS pathway related proteins
Predicted locationi

All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.

  • Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.
  • Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).

The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.

Intracellular
Protein evidence Evidence at protein level (all genes)

HUMAN PROTEIN ATLAS INFORMATIONi

Summary of RNA expression analysis and annotation data generated within the Human Protein Atlas project.

Single cell type
expression clusteri

The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.

Elongating spermatids - Spermiogenesis: Elongation (mainly)
Single cell type specificityi

The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.

Cell type enhanced (Early spermatids, Hofbauer cells, Late primary spermatocytes, Late spermatids, Megakaryocytes, Platelets)
Tissue expression
cluster (RNA)i

The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.

Brain - Synaptic signal transduction (mainly)
Tissue specificity (RNA)i

The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected.

Tissue enhanced (Brain)
Subcellular locationi

Main subcellular location based on data generated in the subcellular section of the Human Protein Atlas.

Not available
Secretome annotationi

All genes with at least one predicted secreted isoform have been annotated and classified with the aim to determine if the corresponding protein(s) are:

  • secreted into blood
  • locally secreted
  • or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.
Not available
GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Chromosome 19
Cytoband q13.32
Chromosome location (bp) 46601074 - 46610782
Number of transcriptsi

Number of protein-coding transcripts from the gene as defined by Ensembl.

7
Ensembl ENSG00000160014 (version 109)
Entrez gene 808
HGNC HGNC:1449
UniProt P0DP25
GeneCards CALM3
ASSAYSi

Links to data of the different assays available in the Structure & Interaction resource of the Human Protein Atlas. Click on the miniature images to directly get to the respective section.

Interaction Metabolic
INTERACTIONi

In the Interaction part of this page network plots showing the gene's first-level interaction partners according to four different datasets are displayed, including a consensus network plot showing only interactions present in at least two of the datasets. By clicking on nodes the network can be expanded. In the network plots the nodes represent genes and edge color represent the number of datasets the interaction belongs to. In-house generated AlphaFold 3 predicted 3D structures for interactions in the consensus network are displayed by clicking on the blue symbols on the edges.

The highlight bar in the top of the plot can be used to color the nodes according to subcellular location (based on data in the Subcellular section), predicted location (based on signalpeptide and transmembrane region predictions), tissue specificity (based on RNA tissue expression profiles) or proteinclass. For genes categorised as single cell type or group specific the option to highlight interaction partners expressed in the same cell type will also be available in the highlight bar.

Custom highlighting of nodes is possible using the top left Filter option in which a query of choice can be built to for example label all nodes that are tissue enriched in both human and mouse brain or those that belongs to a certain tissue expression cluster. The expression cluster for the gene is stated in the box Human Protein Atlas Information above the network plot. Click on Filter in the top left in the plot to find the query builder and some example queries.

Interactions included are direct interaction and physical associations with high and medium confidence from IntAct, physical multivalidated interactions from BioGRID, interactions with>75% probability from BioPlex and significant physical interactions from OpenCell.

Filter menu »
Fields »
e.g. Brain enriched, Localized to mitochondria, Brain - Synaptic signal transduction

Field
Term
Gene name
Class
Subclass
Category
Keyword
Chromosome
External id
Tissue
Cell type
Expression
Antibody panel
Tissue
Main location
Patient ID
Annotation
Tissue
Category
Tau score
Cluster
Reliability
Brain region
Category
Tau score
Brain region
Category
Tau score
Brain region
Category
Tau score
Cluster
Reliability
Tissue
Cell type
Enrichment
Cell type
Category
Tau score
Cell type group
Category
Tau score
Cell type
Category
Tau score
Cell type
Category
Tau score
Cell lineage
Category
Tau score
Cluster
Cluster
Location
Searches
Location
Cell line
Class
Type
Phase
Reliability
Cancer
Prognosis
Cancer
Category
Cancer
Category
Tau score
Cluster
Variants
Interacting gene (ensg_id)
Type
Number of interactions
Pathway
ipTM
Category
Category
Category
Category
Validation
Validation
Validation
Validation
Antibodies
Data type
Column


Consensus
IntAct
BioGrid
OpenCell
BioPlex
Highlight:
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Subcell location
Predicted location
Cell type specificity
Protein class

Non-commercial use only, subject to AlphaFold3 Output Terms of Use

Interaction:
Color scheme:
Confidence
Antibodies
Interactor
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PAE plot
Number of interactions: 6
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
MYO1B3226130
MYO1C3234110
MYO1D1116416
MYO612657150
TBC1D18241180
TBC1D48315130
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 1 View all protein interaction data in IntAct
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
MYO1C3234110
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 36
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
ARRB126355900
ARRB221256800
CSF1R231400
EGFR18727545806
EPHA1000600
EPHA4481800
EPHA5121000
EPHA612700
EPHA7681900
ERBB2325012000
FGFR2572200
FGFR341912300
FGFR4332200
FLT1361200
FLT303900
IGF1R162373115
IQSEC211400
LMTK3011100
MERTK001100
MET6175400
MUSK12600
MYO1B3226130
MYO1C3234110
MYO1D1116416
MYO612657150
NTRK38114000
PDGFRA452700
ROR242418019
ROS1111000
RYK003600
SOCS2345903
STK42317947247
TBC1D18241180
TBC1D48315130
TEK221000
UBE3B115223
Show allShow less
Highlight:
Off
Subcell location
Predicted location
Cell type specificity
Protein class

Number of interactions: 162
Interaction# Consensus# IntAct# BioGrid# OpenCell# BioPlex
ABCD3432072
ABHD10117412
ACTN210661991
ACTR214343614
AIF1L001360
AMOT985761
ANKS6323340
ARHGAP1912340
ARHGEF128317150
ARPC1A910132510
ARPC214523354
ARPC3111623239
ARPC510414145
ARPC5L10514144
ASPM11660
ATP2B1502380
ATP2B4131140
BSG458780
CAMKK113320
CAMKK220840
CAPZA19942128
CAPZA2172461746
CAPZB10061336660
CCDC124015290
CCDC8313240
CCP1109927120
CDC423033160151
CDC73153144105
CEP131662770
CEP290692720
CEP97331870
CETN27814218
CETN3297119
CFL17144464
CTTNBP2NL14102293
CUL76155312
DDX55035313
DENND4A748140
DENND4C601090
DHX309641330
DIDO12317128
DMAP1142740425
EFHD101434
EIF3H201140417
EIF3K16922517
EIF3M14923499
ENSG0000026266000040
ESCO100030
FECH241150
FLNA7188660
FLNB583060
GADD45GIP1159022473
GRAMD1A21490
H1-103018500
H2BC54244254
HIP14481161
HMBOX1376410
HMG20A115327117
INF210990
IQCB1511830
IQGAP110217582
IQGAP3467530
ITPR32213137
ITPRID2561250
KIAA16712212411
KIF1A15840
KIF1C751062
KIF2310949100
LIN7A4121033
LIN7C5516315
LMO75115120
LRCH142970
LRCH223750
LRCH3231490
LRPPRC776882
LRRC5951490130
LRRFIP212550
LUZP1131550
LYAR1729341874
MAGED2212030
MAP7D3011320
MPRIP10827120
MRPL5391314548
MRPS27134331062
MRPS3411033855
MYL100230
MYL611825140
MYO18A311350
MYO1B3226130
MYO1C3234110
MYO1D1116416
MYO1F13234
MYO612657150
MYO9B206150
NEFM5516107
OBSL1426660
OSTF149743
PALS16181733
PDCD47827230
PEAK1011550
PELP191031615
PHKA120240
PHKA2233520
PHKB33640
PHKG2437116
PHLDB2521570
PLEKHG300823
PML121515950
PNN119452418
POLB541292
PPP1R12A2638120
PPP1R9A11550
PPP1R9B64271016
PPP3CA242230
PPP3CB421050
PPP3CC25420
PPP3R201132
PRKAR2A11736134
PRPF33337572621
PSMC63646603313
PSMD113917593913
PSMD72311542016
RACGAP181324110
RAI149526130
RALA431640
RBM2611870
RCAN122720
RPL1044312541135
RPL1355910251192
RPL22L111590
RPL3614876382
RPS103067228120
RPS15A14894462
RPS20255111497
RPS28131043443
RPS4X20131075811
RPS713486522
SCO103720
SH2B132830
SLIRP211936
SPECC1L046717
SPTAN19106370
SRGAP2C00090
STX420373166
SVIL112040
TBC1D18241180
TBC1D48315130
TFAM383450
TIGD101030
TOM1321250
TOM1L222453
TRIM24635280
UBE3C41192621
UBN221861
UNC13B11731
VIM36881091425
VPS13A30960
VPS13C608120
WFS103162220
YAP13132304100
ZCCHC30111522
ZNF53600430
Show allShow less
CALM3 has no defined protein interactions in BioPlex.
METABOLIC SUMMARYi

In this summary the pathway/subsystems to which the gene belongs is shown together with the associated cellular compartment for the reactions based on metabolite information. The number of proteins and metabolites in the pathway is shown as well as the number of reactions for the selected gene. By clicking on a pathway in the summary table the associated metabolic network map is shown, together with a gene-tissue heatmap that shows the expression of genes in that pathway in different tissues.

Gene CALM3 is associated with 1 reactions in 1 different subsystems, and present in the compartments: Cytosol. Provided by metabolicatlas.org
Pathway / Subsystem Subsystem-associated compartments # proteins # metabolites # reactions for
this protein
Isolated Cytosol, Mitochondria, Peroxisome, Endoplasmic reticulum, Extracellular, Nucleus, Golgi apparatus 524 320 1
PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The Splice variant identifier links to the Ensembl website protein summary for the selected splice variant. The data in the Swissprot and TrEMBL columns links to corresponding pages in the UniProt database.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide and number of predicted transmembrane region(s) according to in-house majority decision methods based on sets of predictors are also reported.

Splice variant SwissProt TrEMBL Protein class Length & mass Signal peptide
(predicted)
Transmembrane regions
(predicted)
CALM3-201 P0DP25
B4DJ51
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Disease related genes
Human disease related genes
Mapped to neXtProt
Show all
149 aa
16.8 kDa
No 0
CALM3-202 Q96HY3
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Human disease related genes
113 aa
12.9 kDa
No 0
CALM3-206 Q96HY3
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Human disease related genes
113 aa
12.9 kDa
No 0
CALM3-208 P0DP25
B4DJ51
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Disease related genes
Human disease related genes
Mapped to neXtProt
Show all
149 aa
16.8 kDa
No 0
CALM3-209 M0QZ52
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Human disease related genes
83 aa
9.4 kDa
No 0
CALM3-211 Q96HY3
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Human disease related genes
113 aa
12.9 kDa
No 0
CALM3-212 Q96HY3
Metabolic proteins
Predicted intracellular proteins
RAS pathway related proteins
Human disease related genes
113 aa
12.9 kDa
No 0
Show allShow less

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