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

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:CSF3R

Protein Summary

Gene summary

Gene name: CSF3R
ASpdb.0 ID: 1441
	Gene
Gene symbol	CSF3R
Gene ID	1441
Gene name	colony stimulating factor 3 receptor
Synonyms	CD114\|GCSFR\|SCN7
Cytomap	1p34.3
Type of gene	protein-coding
Description	granulocyte colony-stimulating factor receptorCD114 antigenG-CSF receptorG-CSF-Rcolony stimulating factor 3 receptor (granulocyte)
Modification date	20240403
UniProtAcc	Q99062

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
Q99062-1	Q99062-1_2d9q_B.pdb	2D9Q	X-ray	2.8	B	26	331

ASpdb's canonical and alternatively spliced isoform information.

accession_id

gene_name

canonical_id

alternative_id

canonical_length

alternative_length

canonical_start

canonical_end

type

originalSEQ

variationSEQ

alternative_start

alternative_end

Q99062

CSF3R

Q99062-1

Q99062-2

836

771

622

836

Substitution

EGSELHIILGLFGLLLLLTCLCGTAWLCCSPNRKNPLWPSVPDPAHSSLGSWVPTIMEEDAFQLPGLGTPPITKLTVLEEDEKKPVPWESHNSSETCGLPTLVQTYVLQGDPRAVSTQPQSQSGTSDQVLYGQLLGSPTSPGPGHYLRCDSTQPLLAGLTPSPKSYENLWFQASPLGTLVTPAPSQEDDCVFGPLLNFPLLQGIRVHGMEALGSF

APTGRIPSGQVSQTQLTAAWAPGCPQSWRRMPSSCPALARHPSPSSQCWRRMKRSRCPGSPITAQRPVASPLWSRPMCSRGTQEQFPPSPNPSLAPAIRSFMGSCWAAPQAQGQGTISAVTPLSPSWRASPPAPSPMRTSGSRPAPWGPW

622

771

Q99062

CSF3R

Q99062-1

Q99062-3

836

863

680

Substitution

ELPGPRQGQWLGQTSEMSRALTPHPCVQ

680

707

Q99062

CSF3R

Q99062-1

Q99062-4

836

783

750

783

Substitution

VLYGQLLGSPTSPGPGHYLRCDSTQPLLAGLTPS

AGPPRRSAYFKDQIMLHPAPPNGLLCLFPITSVL

750

783

Q99062

CSF3R

Q99062-1

Q99062-4

836

783

784

836

Deletion

none

783

Multiple sequence alignment of our canonical and alternatively spliced CSF3R

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CSF3R

UniProt-id	ENSG	ENST	ENSP
Q99062-1	ENSG00000119535.20	ENST00000373106.6	ENSP00000362198.2
Q99062-3	ENSG00000119535.20	ENST00000373103.5	ENSP00000362195.1
Q99062-4	ENSG00000119535.20	ENST00000373104.5	ENSP00000362196.1

UniProt-id	NM ID	NP ID
Q99062-1	NM_000760.3	NP_000751.1
Q99062-3	NM_156039.3	NP_724781.1
Q99062-4	NM_172313.2	NP_758519.1

Amino acid sequences of our canonical and alternatively spliced CSF3R

accession_id	Protein sequence
Q99062-1	MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLP HLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKSRGNCQTQGDSILDCVPK DGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSPQLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKCELRH KPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHWSDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVP LEEDSGRIQGYVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVVFSESRGPALTRLHAMARDPHSLWVGWE PPNPWPQGYVIEWGLGPPSASNSNKTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMAPSHAPELHLKHIGK TWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSFSAILNASSRGFVLHGLEPASLYHIHLMAASQAGATNSTVLTLMTLTPEGSELHIIL GLFGLLLLLTCLCGTAWLCCSPNRKNPLWPSVPDPAHSSLGSWVPTIMEEDAFQLPGLGTPPITKLTVLEEDEKKPVPWESHNSSETCGL PTLVQTYVLQGDPRAVSTQPQSQSGTSDQVLYGQLLGSPTSPGPGHYLRCDSTQPLLAGLTPSPKSYENLWFQASPLGTLVTPAPSQEDD
Q99062-2	MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLP HLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKSRGNCQTQGDSILDCVPK DGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSPQLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKCELRH KPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHWSDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVP LEEDSGRIQGYVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVVFSESRGPALTRLHAMARDPHSLWVGWE PPNPWPQGYVIEWGLGPPSASNSNKTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMAPSHAPELHLKHIGK TWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSFSAILNASSRGFVLHGLEPASLYHIHLMAASQAGATNSTVLTLMTLTPAPTGRIPSG QVSQTQLTAAWAPGCPQSWRRMPSSCPALARHPSPSSQCWRRMKRSRCPGSPITAQRPVASPLWSRPMCSRGTQEQFPPSPNPSLAPAIR
Q99062-3	MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLP HLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKSRGNCQTQGDSILDCVPK DGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSPQLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKCELRH KPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHWSDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVP LEEDSGRIQGYVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVVFSESRGPALTRLHAMARDPHSLWVGWE PPNPWPQGYVIEWGLGPPSASNSNKTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMAPSHAPELHLKHIGK TWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSFSAILNASSRGFVLHGLEPASLYHIHLMAASQAGATNSTVLTLMTLTPEGSELHIIL GLFGLLLLLTCLCGTAWLCCSPNRKNPLWPSVPDPAHSSLGSWVPTIMEELPGPRQGQWLGQTSEMSRALTPHPCVQDAFQLPGLGTPPI TKLTVLEEDEKKPVPWESHNSSETCGLPTLVQTYVLQGDPRAVSTQPQSQSGTSDQVLYGQLLGSPTSPGPGHYLRCDSTQPLLAGLTPS
Q99062-4	MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLP HLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKSRGNCQTQGDSILDCVPK DGQSHCCIPRKHLLLYQNMGIWVQAENALGTSMSPQLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLCWEPWQPGLHINQKCELRH KPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHWSDWSPSLELRTTERAPTVRLDTWWRQRQLDPRTVQLFWKPVP LEEDSGRIQGYVVSWRPSGQAGAILPLCNTTELSCTFHLPSEAQEVALVAYNSAGTSRPTPVVFSESRGPALTRLHAMARDPHSLWVGWE PPNPWPQGYVIEWGLGPPSASNSNKTWRMEQNGRATGFLLKENIRPFQLYEIIVTPLYQDTMGPSQHVYAYSQEMAPSHAPELHLKHIGK TWAQLEWVPEPPELGKSPLTHYTIFWTNAQNQSFSAILNASSRGFVLHGLEPASLYHIHLMAASQAGATNSTVLTLMTLTPEGSELHIIL GLFGLLLLLTCLCGTAWLCCSPNRKNPLWPSVPDPAHSSLGSWVPTIMEEDAFQLPGLGTPPITKLTVLEEDEKKPVPWESHNSSETCGL

Protein Functional Features

Main function of this protein. (from UniProt)

CSF3R (go to UniProt):Q99062

Retention 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_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q99062	Topological domain	25	627	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=622;End=836
Q99062	Transmembrane	628	650	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=622;End=836
Q99062	Topological domain	651	836	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=622;End=836
Q99062	Topological domain	651	836	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=680;End=680
Q99062	Topological domain	651	836	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=750;End=783
Q99062	Topological domain	651	836	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=784;End=836
Q99062	Domain	530	623	Note=Fibronectin type-III 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316	Type=Substitution;Start=622;End=836
Q99062	Motif	658	666	Note=Box 1 motif	Type=Substitution;Start=622;End=836

Gene Isoform Structures and Expression Levels for CSF3R

Gene structures of our canonical and alternative spliced genes of CSF3R
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

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 Q99062-1

3D view using mol* of Q99062-2

3D view using mol* of Q99062-3

3D view using mol* of Q99062-4

pLDDT Score Distribution

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 Q99062-1

pLDDT distribution across the protein length of Q99062-2

pLDDT distribution across the protein length of Q99062-3

pLDDT distribution across the protein length of Q99062-4

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of Q99062-1

Ramachandran plot of Q99062-4

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
Q99062-1	1.051	188	1.101	660.618	0.549	0.708	0.908	0.925	0.81	1.142	0.937	435,436,437,438,439,467,468,499,518,519,520,521,52 4,527,549,551,554,555,557,558,559,560,562,580,581, 583,605,723,724,725,726,727,728,729
Q99062-2	1.033	153	1.072	346.087	0.534	0.704	0.919	0.794	0.89	0.892	0.817	333,334,335,336,337,338,339,340,341,342,361,416,41 7,418,420,421,422,423,424,425,457,479,481,507,508, 509,510,511,512
Q99062-3	1.021	150	1.058	363.58	0.568	0.694	0.896	0.541	0.916	0.591	0.98	334,335,336,337,338,339,340,341,342,361,416,417,41 8,420,421,422,423,425,457,479,481,507,508,509,510, 511,512
Q99062-4	1.013	151	1.04	367.696	0.57	0.699	0.891	0.573	0.98	0.585	0.793	332,333,334,335,336,337,338,339,340,341,342,361,41 7,418,420,421,422,423,425,457,458,479,481,507,508, 509,510,511,512

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of Q99062-1_Q99062-1_2d9q_B.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q99062-1_2d9q_B_Q99062-2.pdb

3D view using mol* of Q99062-1_2d9q_B_Q99062-3.pdb

3D view using mol* of Q99062-1_2d9q_B_Q99062-4.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q99062-1_Q99062-2.pdb

3D view using mol* of Q99062-1_Q99062-3.pdb

3D view using mol* of Q99062-1_Q99062-4.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/Q99062-1_vs_Q99062-2.png

./stats/secondary_structure/figure/Q99062-1_vs_Q99062-3.png

./stats/secondary_structure/figure/Q99062-1_vs_Q99062-4.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q99062-1_vs_Q99062-2.png

./stats/relative_asa/Q99062-1_vs_Q99062-3.png

./stats/relative_asa/Q99062-1_vs_Q99062-4.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to CSF3R

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q99062	CSF3R	DB00019	Pegfilgrastim	approved	agonist
Q99062	CSF3R	DB18704	Efbemalenograstim alfa	approved	stimulator
Q99062	CSF3R	DB05249	FavId	investigational
Q99062	CSF3R	DB13144	Lenograstim	approved, investigational	agonist
Q99062	CSF3R	DB13200	Lipegfilgrastim	approved, investigational	agonist
Q99062	CSF3R	DB00099	Filgrastim	approved	stimulator
Q99062	CSF3R	DB15001	Eflapegrastim	approved, investigational	ligand

Related Diseases to CSF3R

Previous studies relating to the alternative splicing of CSF3R and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CSF3R

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance