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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for SPECC1 |
Gene summary |
Gene information | Gene symbol | SPECC1 | Gene ID | 92521 |
Gene name | sperm antigen with calponin homology and coiled-coil domains 1 | |
Synonyms | CYTSB|HCMOGT-1|HCMOGT1|NSP | |
Cytomap | 17p11.2 | |
Type of gene | protein-coding | |
Description | cytospin-BNSP5cytokinesis and spindle organization Bnuclear structure protein 5sperm antigen HCMOGT-1sperm antigen with calponin-like and coiled coil domains 1structure protein NSP5a3astructure protein NSP5a3bstructure protein NSP5b3astructure pr | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for SPECC1 |
Skipped 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
STG | UP | ENST00000261503.9 | SPECC1-201:protein_coding:SPECC1 | 5.060146e+01 | 4.150864e+00 | 6.916585e-04 | 3.183123e-02 |
CB | DOWN | ENST00000492188.1 | SPECC1-210:retained_intron:SPECC1 | 2.894149e+01 | -2.233463e+00 | 3.636128e-07 | 6.339224e-06 |
TC | DOWN | ENST00000492188.1 | SPECC1-210:retained_intron:SPECC1 | 4.500842e+01 | -3.023529e+00 | 1.902334e-13 | 8.840454e-11 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SPECC1 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_164001 | chr17 | 20156224:20156236:20204333:20205912:20227413:20227620 | 20204333:20205912 |
exon_skip_168175 | chr17 | 20017987:20018102:20057677:20057817:20096631:20096715 | 20057677:20057817 |
exon_skip_207564 | chr17 | 20260192:20260294:20296961:20297077:20306023:20306082 | 20296961:20297077 |
exon_skip_217880 | chr17 | 20009363:20009424:20017987:20018102:20096631:20096798 | 20017987:20018102 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for SPECC1 |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000261503 | 20296961 | 20297077 | In-frame |
ENST00000395527 | 20296961 | 20297077 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000261503 | 20296961 | 20297077 | In-frame |
ENST00000395527 | 20296961 | 20297077 | In-frame |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000261503 | 20296961 | 20297077 | In-frame |
ENST00000395527 | 20296961 | 20297077 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPECC1 |
p-ENSG00000128487_img4.png |
Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000261503 | 3965 | 1068 | 20296961 | 20297077 | 2993 | 3108 | 980 | 1019 |
ENST00000395527 | 3380 | 1068 | 20296961 | 20297077 | 3025 | 3140 | 980 | 1019 |
Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000261503 | 3965 | 1068 | 20296961 | 20297077 | 2993 | 3108 | 980 | 1019 |
ENST00000395527 | 3380 | 1068 | 20296961 | 20297077 | 3025 | 3140 | 980 | 1019 |
Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000261503 | 3965 | 1068 | 20296961 | 20297077 | 2993 | 3108 | 980 | 1019 |
ENST00000395527 | 3380 | 1068 | 20296961 | 20297077 | 3025 | 3140 | 980 | 1019 |
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 feature | Description of feature |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
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 feature | Description of feature |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
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 feature | Description of feature |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 785 | 1068 | Alternative sequence | ID=VSP_021163;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 791 | 1068 | Alternative sequence | ID=VSP_021165;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15602574,ECO:0000303|Ref.1;Dbxref=PMID:15602574 |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 1 | 1068 | Chain | ID=PRO_0000254033;Note=Cytospin-B |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
Q5M775 | 980 | 1019 | 962 | 1067 | Domain | Note=Calponin-homology (CH);Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00044 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SPECC1 |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for SPECC1 |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- Non-synonymous mutations located in the skipped exons in CCLE. |
Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for SPECC1 |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPECC1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_217880 | rs17604987 | chr17:19964018 | 8.792515e-06 | 1.125052e-03 |
HCC | exon_skip_217880 | rs1638527 | chr17:19942080 | 8.930968e-06 | 1.138949e-03 |
HCC | exon_skip_217880 | rs7209653 | chr17:19978771 | 1.048195e-04 | 9.529578e-03 |
HCC | exon_skip_217880 | rs17759609 | chr17:20089201 | 5.969260e-04 | 3.894725e-02 |
PCC | exon_skip_217880 | rs7209653 | chr17:19978771 | 1.333513e-04 | 2.161101e-02 |
PCC | exon_skip_217880 | rs12453720 | chr17:19991889 | 1.344504e-04 | 2.174645e-02 |
PCC | exon_skip_217880 | rs17759609 | chr17:20089201 | 2.673352e-04 | 3.756133e-02 |
PCC | exon_skip_217880 | rs4925075 | chr17:20066422 | 2.729144e-04 | 3.800322e-02 |
PCC | exon_skip_217880 | rs4925078 | chr17:20079160 | 2.729144e-04 | 3.800322e-02 |
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Correlation with RNA binding proteins (RBPs) for SPECC1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
IFG | TRNAU1AP | exon_skip_168175 | -4.759142e-01 | 1.209972e-02 |
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RelatedDrugs for SPECC1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SPECC1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |