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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for CALD1

check button Gene summary
Gene informationGene symbol

CALD1

Gene ID

800

Gene namecaldesmon 1
SynonymsCDM|H-CAD|HCAD|L-CAD|LCAD|NAG22
Cytomap

7q33

Type of geneprotein-coding
Descriptioncaldesmontestis secretory sperm-binding protein Li 227n
Modification date20200313
UniProtAcc

A0A140VKA0,

C9J813,

C9JE79,

C9JEK3,

E7EX44,

E9PGZ1,

F8WE61,

Q05DR4,

Q6P707,

Q6PJM5,

Q9NYG1,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Gene structures and expression levels for CALD1

check buttonSkipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

ENSG00000122786
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
STGUPENST00000361675.7CALD1-201:protein_coding:CALD17.961214e+011.707350e+006.593621e-062.097919e-03
STGUPENST00000422748.5CALD1-205:protein_coding:CALD11.661274e+011.174241e+006.273744e-043.039496e-02
CBUPENST00000422748.5CALD1-205:protein_coding:CALD12.689817e+019.854477e-014.831101e-078.079917e-06
CBUPENST00000466704.1CALD1-214:lncRNA:CALD11.077654e+018.886747e-013.466286e-064.313079e-05
CBUPENST00000480638.1CALD1-219:retained_intron:CALD14.635115e+008.935563e-013.910373e-053.338719e-04
TCUPENST00000422748.5CALD1-205:protein_coding:CALD15.164042e+011.312279e+004.388580e-121.270896e-09
TCUPENST00000466704.1CALD1-214:lncRNA:CALD11.818984e+011.130474e+007.133643e-109.913095e-08
TCUPENST00000361901.6CALD1-202:protein_coding:CALD11.390451e+038.370005e-015.280360e-072.409904e-05
TCUPENST00000436461.6CALD1-209:protein_coding:CALD11.786009e+002.144449e+007.742265e-034.636663e-02

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CALD1

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_114047chr7134933879:134934077:134935688:134935765:134941092:134941237134935688:134935765
exon_skip_1626chr7134779715:134779749:134809591:134809627:134843884:134843971134809591:134809627
exon_skip_191964chr7134933837:134934077:134935688:134935765:134941092:134941237134935688:134935765
exon_skip_214197chr7134932988:134934077:134935688:134935765:134941092:134941237134935688:134935765
exon_skip_227310chr7134933194:134933390:134935688:134935765:134941092:134941237134935688:134935765
exon_skip_240599chr7134941182:134941237:134947508:134947769:134950374:134950514134947508:134947769
exon_skip_269660chr7134891610:134891673:134928754:134928900:134932988:134933123134928754:134928900
exon_skip_51558chr7134960533:134960628:134962820:134962934:134965306:134965386134962820:134962934
exon_skip_62403chr7134933194:134933390:134935688:134935765:134941092:134941108134935688:134935765
exon_skip_89747chr7134867693:134867804:134928049:134928090:134928754:134928900134928049:134928090

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
psi tcga
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value
exon_skip_51558MSBB_PG1.527407e-012.561538e-01-1.034131e-012.909178e-04
exon_skip_51558Mayo_TC1.456098e-012.651282e-01-1.195184e-015.340071e-07


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Open reading frame (ORF) annotation in the exon skipping event for CALD1

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000361675134935688134935765In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000361675134947508134947769Frame-shift
ENST00000361675134935688134935765In-frame

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Infer the effects of exon skipping event on protein functional features for CALD1

p-ENSG00000122786_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000361675362979313493568813493576515391615436462

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000361675362979313493568813493576515391615436462

check button Lost protein functional features of individual exon skipping events in ROSMAP.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q05682436462208462Alternative sequenceID=VSP_004156;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:1465449,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:1555769,ECO:0000303|PubMed:1885618;Dbxref=PMID:1465449,
Q05682436462208436Alternative sequenceID=VSP_004155;Note=In isoform 2%2C isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:1465449,ECO:0000303|PubMed:14702039;Dbxref=PMID:1465449,PMID:14702039
Q056824364621793ChainID=PRO_0000089288;Note=Caldesmon
Q05682436462459459Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733

check button Lost protein functional features of individual exon skipping events in MSBB.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature

check button Lost protein functional features of individual exon skipping events in Mayo.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q05682436462208462Alternative sequenceID=VSP_004156;Note=In isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:1465449,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:1555769,ECO:0000303|PubMed:1885618;Dbxref=PMID:1465449,
Q05682436462208436Alternative sequenceID=VSP_004155;Note=In isoform 2%2C isoform 3 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:1465449,ECO:0000303|PubMed:14702039;Dbxref=PMID:1465449,PMID:14702039
Q056824364621793ChainID=PRO_0000089288;Note=Caldesmon
Q05682436462459459Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733


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3'-UTR located exon skipping events that lost miRNA binding sites in CALD1

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for CALD1

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for CALD1

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CALD1

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for CALD1

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBELAVL4exon_skip_515584.478278e-013.638790e-09
CBNUP42exon_skip_515586.185881e-014.680955e-18
CBRALYLexon_skip_515586.018473e-016.092633e-17
CBPTBP3exon_skip_515584.060514e-011.201279e-07
DLPFCELAVL4exon_skip_515584.527211e-012.481785e-18
DLPFCKHDRBS2exon_skip_515585.836023e-015.767826e-32
FLELAVL4exon_skip_515586.117096e-011.110488e-20
FLILF2exon_skip_515584.781848e-013.920633e-12
FLKHDRBS2exon_skip_515584.209444e-011.798419e-09
FLPUF60exon_skip_515584.176323e-012.478805e-09
FLNUP42exon_skip_515584.010409e-011.174770e-08
FLRALYLexon_skip_515585.977877e-011.341573e-19
FLPTBP1exon_skip_51558-4.140257e-013.501690e-09
FLNOVA1exon_skip_515584.981669e-013.480167e-13
HCCPTBP1exon_skip_51558-5.961609e-011.449173e-27
HCCHNRNPFexon_skip_51558-5.500147e-016.591563e-23
PCCELAVL4exon_skip_515584.526129e-012.960266e-12
PCCPTBP1exon_skip_51558-6.760827e-014.503787e-30
PCCHNRNPFexon_skip_51558-5.909394e-011.240249e-21
PGELAVL4exon_skip_515586.791467e-011.222303e-26
PGILF2exon_skip_515585.703504e-011.583798e-17
PGKHDRBS2exon_skip_515585.365637e-012.469371e-15
PGPUF60exon_skip_515584.537138e-016.968054e-11
PGNUP42exon_skip_515584.221280e-011.771956e-09
PGRALYLexon_skip_515586.332217e-012.381311e-22
PGNOVA1exon_skip_515585.500963e-013.498376e-16
STGELAVL4exon_skip_515586.750266e-011.394602e-12
STGILF2exon_skip_515585.656072e-011.697365e-08
STGKHDRBS2exon_skip_515585.596761e-012.570758e-08
STGPUF60exon_skip_515584.856543e-012.461502e-06
STGNUP42exon_skip_515585.712869e-011.131821e-08
STGRALYLexon_skip_515586.658782e-013.562427e-12
STGPTBP3exon_skip_515585.108439e-015.875410e-07
STGNOVA1exon_skip_515585.677502e-011.458008e-08
TCELAVL4exon_skip_515584.465275e-013.252193e-09
TCILF2exon_skip_515584.249382e-012.134896e-08
TCKHDRBS2exon_skip_515584.507461e-012.216795e-09
TCNUP42exon_skip_515584.485737e-012.702249e-09
TCRALYLexon_skip_515584.745830e-012.298365e-10
TCPTBP1exon_skip_51558-4.391986e-016.251929e-09
TCNOVA1exon_skip_515587.102203e-017.284210e-26

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RelatedDrugs for CALD1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CALD1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource