ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures
ASpdb Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Protein Summary

leaf

AS Summary

leaf

Protein Functional Features

leaf

Gene Isoform Structures and Expression Levels

leaf

Protein Structures

leaf

pLDDT Score Distribution

leaf

Ramachandran Plot of Protein Structures

leaf

Potential Active Site Information

leaf

Protein Structure and Feature Comparision

leaf

Protein-Protein Interaction

leaf

Related Drugs

leaf

Related Diseases

leaf

Clinically Important Variants

Protein:SREBF1

Protein Summary

check button Gene summary
Gene name: SREBF1
ASpdb.0 ID: 6720
Gene
Gene symbol

SREBF1

Gene ID

6720

Gene namesterol regulatory element binding transcription factor 1
SynonymsHMD|IFAP2|SREBP1|bHLHd1
Cytomap

17p11.2

Type of geneprotein-coding
Descriptionsterol regulatory element-binding protein 1class D basic helix-loop-helix protein 1
Modification date20240407
UniProtAcc

P36956


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneSREBF1

GO:0000977

RNA polymerase II transcription regulatory region sequence-specific DNA binding

23610160

GeneSREBF1

GO:0000981

DNA-binding transcription factor activity, RNA polymerase II-specific

12177166

GeneSREBF1

GO:0001228

DNA-binding transcription activator activity, RNA polymerase II-specific

31501273

GeneSREBF1

GO:0003700

DNA-binding transcription factor activity

16407292

GeneSREBF1

GO:0004879

nuclear receptor activity

23610160

GeneSREBF1

GO:0005634

nucleus

15358760

GeneSREBF1

GO:0032810

sterol response element binding

16407292|31501273

GeneSREBF1

GO:0032933

SREBP signaling pathway

27614840

GeneSREBF1

GO:0045542

positive regulation of cholesterol biosynthetic process

12177166

GeneSREBF1

GO:0045944

positive regulation of transcription by RNA polymerase II

26437365|31501273

GeneSREBF1

GO:0090209

negative regulation of triglyceride metabolic process

28483554

GeneSREBF1

GO:1902895

positive regulation of miRNA transcription

31501273

GeneSREBF1

GO:1990837

sequence-specific double-stranded DNA binding

28473536



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
P36956-1P36956-1_1am9_C.pdb1AM9X-ray2.3C319400

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
P36956SREBF1P36956-1P36956-311471047129SubstitutionMDEPPFSEAALEQALGEPCDLDAALLTDIMDCTF15
P36956SREBF1P36956-1P36956-31147104710351147SubstitutionVFLHEATARLMAGASPTRTHQLLDRSLRRRAGPGGKGGAVAELEPRPTRREHAEALLLASCYLPPGFLSAPGQRVGMLAEAARTLEKLGDRRLLHDCQQMLMRLGGGTTVTSSLMDVLTSESAWALPQHLGKGFPSPSGHKVPGWHGRMD10111047
P36956SREBF1P36956-1P36956-51147470469470SubstitutionAKTE469470
P36956SREBF1P36956-1P36956-511474704711147Deletionnonenone470470
P36956SREBF1P36956-1P36956-61147446129SubstitutionMDEPPFSEAALEQALGEPCDLDAALLTDIMDCTF15
P36956SREBF1P36956-1P36956-61147446469470SubstitutionAKTE445446
P36956SREBF1P36956-1P36956-611474464711147Deletionnonenone446446

check buttonMultiple sequence alignment of our canonical and alternatively spliced SREBF1

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SREBF1
UniProt-idENSGENSTENSP
P36956-1ENSG00000072310.18ENST00000261646.11ENSP00000261646.5

UniProt-idNM IDNP ID
P36956-1NM_004176.4NP_004167.3

check buttonAmino acid sequences of our canonical and alternatively spliced SREBF1
accession_idProtein sequence
P36956-1MDEPPFSEAALEQALGEPCDLDAALLTDIEDMLQLINNQDSDFPGLFDPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGP
QAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGN
TQQPLPGLPLASPPGVPPVSLHTQVQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLLLTAMKTDGATVKAAGLSPL
VSGTTVQTGPLPTLVSGGTILATVPLVVDAEKLPINRLAAGSKAPASAQSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKS
AVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLKDLVSACGSGGNTDVLMEGVKTEVEDTLTPPPSDAGSPFQSSPLSLGSRGSGS
GGSGSDSEPDSPVFEDSKAKPEQRPSLHSRGMLDRSRLALCTLVFLCLSCNPLASLLGARGLPSPSDTTSVYHSPGRNVLGTESRDGPGW
AQWLLPPVVWLLNGLLVLVSLVLLFVYGEPVTRPHSGPAVYFWRHRKQADLDLARGDFAQAAQQLWLALRALGRPLPTSHLDLACSLLWN
LIRHLLQRLWVGRWLAGRAGGLQQDCALRVDASASARDAALVYHKLHQLHTMGKHTGGHLTATNLALSALNLAECAGDAVSVATLAEIYV
AAALRVKTSLPRALHFLTRFFLSSARQACLAQSGSVPPAMQWLCHPVGHRFFVDGDWSVLSTPWESLYSLAGNPVDPLAQVTQLFREHLL
ERALNCVTQPNPSPGSADGDKEFSDALGYLQLLNSCSDAAGAPAYSFSISSSMATTTGVDPVAKWWASLTAVVIHWLRRDEEAAERLCPL
VEHLPRVLQESERPLPRAALHSFKAARALLGCAKAESGPASLTICEKASGYLQDSLATTPASSSIDKAVQLFLCDLLLVVRTSLWRQQQP
PAPAPAAQGTSSRPQASALELRGFQRDLSSLRRLAQSFRPAMRRVFLHEATARLMAGASPTRTHQLLDRSLRRRAGPGGKGGAVAELEPR
P36956-3MDCTFEDMLQLINNQDSDFPGLFDPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMP
AFSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQ
VQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLLLTAMKTDGATVKAAGLSPLVSGTTVQTGPLPTLVSGGTILATV
PLVVDAEKLPINRLAAGSKAPASAQSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN
LSLRTAVHKSKSLKDLVSACGSGGNTDVLMEGVKTEVEDTLTPPPSDAGSPFQSSPLSLGSRGSGSGGSGSDSEPDSPVFEDSKAKPEQR
PSLHSRGMLDRSRLALCTLVFLCLSCNPLASLLGARGLPSPSDTTSVYHSPGRNVLGTESRDGPGWAQWLLPPVVWLLNGLLVLVSLVLL
FVYGEPVTRPHSGPAVYFWRHRKQADLDLARGDFAQAAQQLWLALRALGRPLPTSHLDLACSLLWNLIRHLLQRLWVGRWLAGRAGGLQQ
DCALRVDASASARDAALVYHKLHQLHTMGKHTGGHLTATNLALSALNLAECAGDAVSVATLAEIYVAAALRVKTSLPRALHFLTRFFLSS
ARQACLAQSGSVPPAMQWLCHPVGHRFFVDGDWSVLSTPWESLYSLAGNPVDPLAQVTQLFREHLLERALNCVTQPNPSPGSADGDKEFS
DALGYLQLLNSCSDAAGAPAYSFSISSSMATTTGVDPVAKWWASLTAVVIHWLRRDEEAAERLCPLVEHLPRVLQESERPLPRAALHSFK
AARALLGCAKAESGPASLTICEKASGYLQDSLATTPASSSIDKAVQLFLCDLLLVVRTSLWRQQQPPAPAPAAQGTSSRPQASALELRGF
P36956-5MDEPPFSEAALEQALGEPCDLDAALLTDIEDMLQLINNQDSDFPGLFDPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGP
QAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGN
TQQPLPGLPLASPPGVPPVSLHTQVQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLLLTAMKTDGATVKAAGLSPL
VSGTTVQTGPLPTLVSGGTILATVPLVVDAEKLPINRLAAGSKAPASAQSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKS
AVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLKDLVSACGSGGNTDVLMEGVKTEVEDTLTPPPSDAGSPFQSSPLSLGSRGSGS
P36956-6MDCTFEDMLQLINNQDSDFPGLFDPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMP
AFSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQ
VQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLLLTAMKTDGATVKAAGLSPLVSGTTVQTGPLPTLVSGGTILATV
PLVVDAEKLPINRLAAGSKAPASAQSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
SREBF1 (go to UniProt):P36956

check buttonRetention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Substitution;Start=1;End=29
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Substitution;Start=469;End=470
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Substitution;Start=1;End=29
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Substitution;Start=469;End=470
P36956Topological domain1487Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Transmembrane488508Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Transmembrane488508Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Topological domain509547Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Topological domain509547Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Transmembrane548568Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Transmembrane548568Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Topological domain5691147Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Substitution;Start=1035;End=1147
P36956Topological domain5691147Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Topological domain5691147Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255Type=Deletion;Start=471;End=1147
P36956Region160Note=Transcriptional activation (acidic);Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:8402897;Dbxref=PMID:8402897Type=Substitution;Start=1;End=29
P36956Region160Note=Transcriptional activation (acidic);Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:8402897;Dbxref=PMID:8402897Type=Substitution;Start=1;End=29
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Substitution;Start=469;End=470
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Deletion;Start=471;End=1147
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Substitution;Start=469;End=470
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Deletion;Start=471;End=1147
P36956Region421479Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=469;End=470
P36956Region421479Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=471;End=1147
P36956Region421479Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=469;End=470
P36956Region421479Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=471;End=1147
P36956Motif2735Note=9aaTAD;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:31375868;Dbxref=PMID:31375868Type=Substitution;Start=1;End=29
P36956Motif2735Note=9aaTAD;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:31375868;Dbxref=PMID:31375868Type=Substitution;Start=1;End=29
P36956Compositional bias461479Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=469;End=470
P36956Compositional bias461479Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=471;End=1147
P36956Compositional bias461479Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Substitution;Start=469;End=470
P36956Compositional bias461479Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=471;End=1147


Gene Isoform Structures and Expression Levels for SREBF1

check buttonGene structures of our canonical and alternative spliced genes of SREBF1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of SREBF1

check button Expression levels of gene isoforms across GTEx.
gtex expression

check button Expression levels of gene isoforms across TCGA.
tcga expression


Protein Structures

check button PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
3D view using mol* of P36956-1
3D view using mol* of P36956-3
3D view using mol* of P36956-5
3D view using mol* of P36956-6


pLDDT Score Distribution

check button pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
pLDDT distribution across the protein length of P36956-1
all structure
pLDDT distribution across the protein length of P36956-3
all structure
pLDDT distribution across the protein length of P36956-5
all structure
pLDDT distribution across the protein length of P36956-6
all structure


Ramachandran Plot of Protein Structures


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.
Ramachandran plot of P36956-1
all structure
Ramachandran plot of P36956-3
all structure
Ramachandran plot of P36956-5
all structure
Ramachandran plot of P36956-6
all structure

Potential Active Site Information


check button The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.
UniProt-idSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
P36956-11.1331230.958240.4430.4170.8971.2820.3151.5950.1970.932675,757,758,759,762,790,791,792,793,794,796,798,79
9,802,803,806,846,849,850,851,852,853,854,855,856,
857,858,860,861,862,863,865,866,867,868,869,870
P36956-31.0552191.055443.1560.3930.781.0840.6571.0850.6060.94450,451,452,453,455,456,458,459,460,461,463,546,55
4,557,561,582,583,586,587,589,590,591,592,593,594,
598,602,605,606,609,649,670,674,677,678
P36956-50.51110.48245.6190.8590.5290.5990.710.4521.5690.515340,343,344,347,357,359,362
P36956-60.503130.43736.3580.8190.5740.8540.6170.7560.8160.78113,16,350,353,354,357

Protein Structure and Feature Comparision


check button Protein Structure Comparision Using Template Modeling Scores (TM-score).
all structure

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)
3D view using mol* of P36956-1_P36956-1_1am9_C.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of P36956-1_1am9_C_P36956-3.pdb
3D view using mol* of P36956-1_1am9_C_P36956-5.pdb
3D view using mol* of P36956-1_1am9_C_P36956-6.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of P36956-1_P36956-3.pdb
3D view using mol* of P36956-1_P36956-5.pdb
3D view using mol* of P36956-1_P36956-6.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/P36956-1_vs_P36956-3.png
all structure<
./stats/secondary_structure/figure/P36956-1_vs_P36956-5.png
all structure<
./stats/secondary_structure/figure/P36956-1_vs_P36956-6.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/P36956-1_vs_P36956-3.png
all structure<
./stats/relative_asa/P36956-1_vs_P36956-5.png
all structure<
./stats/relative_asa/P36956-1_vs_P36956-6.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Substitution;Start=469;End=470
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Deletion;Start=471;End=1147
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Substitution;Start=469;End=470
P36956Region234497Note=Interaction with LMNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9WTN3Type=Deletion;Start=471;End=1147


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to SREBF1


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions
P36956SREBF1DB11133Omega-3 fatty acidsapproved, nutraceuticalinhibitor
P36956SREBF1DB13961Fish oilapproved, nutraceuticalregulator
P36956SREBF1DB03756Doconexentapproved, investigationalinhibitor
P36956SREBF1DB09539Omega-3-acid ethyl estersapproved, investigationalinhibitor

Related Diseases to SREBF1


check button Previous studies relating to the alternative splicing of SREBF1 and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term


Clinically important variants in SREBF1


check button (ClinVar, 04/20/2024)
accession_iduniprot_idgene_nameTypeVariantClinical_significance