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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for HMGN1 |
 Gene summary |
| Gene information | Gene symbol | HMGN1 | Gene ID | 3150 |
| Gene name | high mobility group nucleosome binding domain 1 | |
| Synonyms | HMG14 | |
| Cytomap | 21q22.2 | |
| Type of gene | protein-coding | |
| Description | non-histone chromosomal protein HMG-14high mobility group nucleosome-binding domain-containing protein 1high-mobility group (nonhistone chromosomal) protein 14high-mobility group nucleosome binding 1nonhistone chromosomal protein HMG-14 | |
| Modification date | 20200320 | |
| UniProtAcc | A0A494C035, | |
| 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 HMGN1 |
| 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. |
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ENSG00000205581
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| DLPFC | DOWN | ENST00000471260.1 | HMGN1-211:lncRNA:HMGN1 | 1.795566e+00 | -1.139202e+00 | 1.753934e-03 | 4.853034e-02 |
| CB | DOWN | ENST00000288344.14 | HMGN1-201:nonsense_mediated_decay:HMGN1 | 2.936962e+02 | -2.139525e+00 | 7.932487e-11 | 5.200878e-09 |
| CB | DOWN | ENST00000492280.5 | HMGN1-220:retained_intron:HMGN1 | 6.685372e+02 | -9.226937e-01 | 3.096001e-07 | 5.526144e-06 |
| CB | DOWN | ENST00000479586.5 | HMGN1-212:lncRNA:HMGN1 | 2.768540e+01 | -9.207053e-01 | 1.451124e-02 | 4.697330e-02 |
| TC | DOWN | ENST00000288344.14 | HMGN1-201:nonsense_mediated_decay:HMGN1 | 1.322124e+02 | -1.627207e+00 | 1.256902e-08 | 1.092195e-06 |
| TC | UP | ENST00000490032.5 | HMGN1-218:lncRNA:HMGN1 | 1.905467e+01 | 9.058845e-01 | 2.756903e-03 | 2.139392e-02 |
| TC | DOWN | ENST00000479586.5 | HMGN1-212:lncRNA:HMGN1 | 2.345159e+01 | -8.841277e-01 | 3.145271e-03 | 2.365376e-02 |
| 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 HMGN1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_113422 | chr21 | 39347247:39347292:39347379:39347483:39347916:39347952 | 39347379:39347483 |
| exon_skip_12354 | chr21 | 39347447:39347483:39347916:39347952:39348292:39348339 | 39347916:39347952 |
| exon_skip_136884 | chr21 | 39345217:39345274:39347379:39347478:39348292:39348339 | 39347379:39347478 |
| exon_skip_158112 | chr21 | 39345146:39345274:39345830:39345958:39348292:39348339 | 39345830:39345958 |
| exon_skip_182630 | chr21 | 39347247:39347292:39347379:39347483:39348292:39348339 | 39347379:39347483 |
| exon_skip_189515 | chr21 | 39345217:39345274:39347247:39347292:39347379:39347478 | 39347247:39347292 |
| exon_skip_190757 | chr21 | 39345146:39345274:39345830:39345958:39347379:39347474 | 39345830:39345958 |
| exon_skip_231172 | chr21 | 39345146:39345274:39347379:39347478:39348292:39348339 | 39347379:39347478 |
| exon_skip_245503 | chr21 | 39345217:39345274:39347247:39347292:39348292:39348339 | 39347247:39347292 |
| exon_skip_24815 | chr21 | 39345217:39345274:39345830:39345958:39347379:39347478 | 39345830:39345958 |
| exon_skip_249751 | chr21 | 39345217:39345274:39345830:39345958:39347247:39347292 | 39345830:39345958 |
| exon_skip_255556 | chr21 | 39345146:39345274:39347247:39347292:39348292:39348339 | 39347247:39347292 |
| exon_skip_260691 | chr21 | 39345217:39345274:39345830:39347292:39347379:39347478 | 39345830:39347292 |
| exon_skip_264600 | chr21 | 39345146:39345274:39345830:39347292:39347379:39347478 | 39345830:39347292 |
| exon_skip_270380 | chr21 | 39345146:39345274:39345830:39345958:39347379:39347478 | 39345830:39345958 |
| exon_skip_276545 | chr21 | 39345217:39345274:39345830:39345958:39348292:39348339 | 39345830:39345958 |
| exon_skip_284245 | chr21 | 39345217:39345274:39347379:39347483:39348292:39348339 | 39347379:39347483 |
| exon_skip_29530 | chr21 | 39348292:39348339:39348422:39348451:39348545:39348577 | 39348422:39348451 |
| exon_skip_31855 | chr21 | 39345830:39345958:39347247:39347292:39347379:39347478 | 39347247:39347292 |
| exon_skip_35998 | chr21 | 39345830:39345958:39347114:39347292:39347379:39347478 | 39347114:39347292 |
| exon_skip_56500 | chr21 | 39347379:39347483:39347916:39347952:39348292:39348339 | 39347916:39347952 |
| exon_skip_58361 | chr21 | 39345146:39345274:39345830:39345958:39347247:39347292 | 39345830:39345958 |
| exon_skip_61162 | chr21 | 39345830:39345958:39347379:39347483:39348292:39348339 | 39347379:39347483 |
| exon_skip_82122 | chr21 | 39345830:39345958:39347379:39347478:39348292:39348339 | 39347379:39347478 |
| exon_skip_82555 | chr21 | 39345146:39345274:39347247:39347292:39347379:39347478 | 39347247:39347292 |
| exon_skip_98560 | chr21 | 39345146:39345274:39348292:39348339:39348422:39348451 | 39348292:39348339 |
| exon_skip_99566 | chr21 | 39345146:39345274:39347379:39347483:39348292:39348339 | 39347379:39347483 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_264600 | Mayo_CB | 5.479710e-01 | 6.711864e-01 | -1.232154e-01 | 3.275222e-04 |
| exon_skip_56500 | Mayo_TC | 4.109375e-01 | 5.271186e-01 | -1.161811e-01 | 8.820143e-03 |
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Open reading frame (ORF) annotation in the exon skipping event for HMGN1 |
| 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 |
| ENST00000380749 | 39348422 | 39348451 | 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 |
| 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 |
| ENST00000380749 | 39348292 | 39348339 | In-frame |
| ENST00000380749 | 39348422 | 39348451 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HMGN1 |
p-ENSG00000205581_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 |
| ENST00000380749 | 1400 | 100 | 39348422 | 39348451 | 332 | 360 | 16 | 25 |
| 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 |
| 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 |
| ENST00000380749 | 1400 | 100 | 39348422 | 39348451 | 332 | 360 | 16 | 25 |
| ENST00000380749 | 1400 | 100 | 39348292 | 39348339 | 362 | 408 | 26 | 41 |
| 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 |
| P05114 | 16 | 25 | 1 | 100 | Chain | ID=PRO_0000206691;Note=Non-histone chromosomal protein HMG-14 |
| P05114 | 16 | 25 | 21 | 21 | Modified residue | Note=Phosphoserine%3B by RPS6KA5;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:23186163,ECO:0000269|PubMed:10739259;Dbxref=PMID:23186163,PMID:10739259 |
| P05114 | 16 | 25 | 25 | 25 | Modified residue | Note=ADP-ribosylserine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28190768;Dbxref=PMID:28190768 |
| P05114 | 16 | 25 | 25 | 25 | Modified residue | Note=Phosphoserine%3B alternate%3B by RPS6KA5;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:23186163,ECO:0000269|PubMed:10739259;Dbxref=PMID:23186163,PMID:10739259 |
| 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 |
| 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 |
| P05114 | 16 | 25 | 1 | 100 | Chain | ID=PRO_0000206691;Note=Non-histone chromosomal protein HMG-14 |
| P05114 | 16 | 25 | 21 | 21 | Modified residue | Note=Phosphoserine%3B by RPS6KA5;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:23186163,ECO:0000269|PubMed:10739259;Dbxref=PMID:23186163,PMID:10739259 |
| P05114 | 16 | 25 | 25 | 25 | Modified residue | Note=ADP-ribosylserine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:28190768;Dbxref=PMID:28190768 |
| P05114 | 16 | 25 | 25 | 25 | Modified residue | Note=Phosphoserine%3B alternate%3B by RPS6KA5;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:23186163,ECO:0000269|PubMed:10739259;Dbxref=PMID:23186163,PMID:10739259 |
| P05114 | 26 | 41 | 1 | 100 | Chain | ID=PRO_0000206691;Note=Non-histone chromosomal protein HMG-14 |
| P05114 | 26 | 41 | 27 | 27 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P18608 |
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3'-UTR located exon skipping events that lost miRNA binding sites in HMGN1 |
| 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 HMGN1 |
| - 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 HMGN1 |
| 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 HMGN1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for HMGN1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | U2AF2 | exon_skip_264600 | -4.285394e-01 | 4.500692e-07 |
| CB | RBM3 | exon_skip_264600 | 4.314056e-01 | 3.697090e-07 |
| CB | RBM45 | exon_skip_264600 | 4.278342e-01 | 4.722511e-07 |
| CB | ZNF638 | exon_skip_253477 | -4.215879e-01 | 3.125674e-08 |
| CB | RBM6 | exon_skip_253477 | -4.235781e-01 | 2.649815e-08 |
| CB | U2AF2 | exon_skip_253477 | -5.248471e-01 | 1.233212e-12 |
| CB | PCBP4 | exon_skip_253477 | 5.123803e-01 | 5.059514e-12 |
| CB | SNRPA | exon_skip_253477 | -4.340562e-01 | 1.091019e-08 |
| CB | RBM45 | exon_skip_253477 | 5.889499e-01 | 3.207070e-16 |
| CB | RBM4 | exon_skip_253477 | -6.173935e-01 | 4.431007e-18 |
| TC | PCBP4 | exon_skip_235954 | 5.221293e-01 | 1.433428e-12 |
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RelatedDrugs for HMGN1 |
| 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 HMGN1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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