Protein:SEMA4D |
Protein Summary |
 Gene summary |
| Gene name: SEMA4D | ASpdb.0 ID: 10507 | Gene | Gene symbol | SEMA4D | Gene ID | 10507 |
| Gene name | semaphorin 4D |
| Synonyms | A8|BB18|C9orf164|CD100|COLL4|GR3|M-sema-G|SEMAJ|coll-4 |
| Cytomap | 9q22.2 |
| Type of gene | protein-coding |
| Description | semaphorin-4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4D |
| Modification date | 20240411 |
| UniProtAcc | Q92854 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | SEMA4D | GO:0001934 | positive regulation of protein phosphorylation | 16055703 |
| Gene | SEMA4D | GO:0005102 | signaling receptor binding | 11254688|20877282 |
| Gene | SEMA4D | GO:0005886 | plasma membrane | 8876214 |
| Gene | SEMA4D | GO:0007162 | negative regulation of cell adhesion | 15218527 |
| Gene | SEMA4D | GO:0030335 | positive regulation of cell migration | 16055703 |
| Gene | SEMA4D | GO:0038023 | signaling receptor activity | 15613544 |
| Gene | SEMA4D | GO:0071526 | semaphorin-plexin signaling pathway | 15218527 |
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 |
| Q92854-1 | Q92854-1_1olz_A.pdb | 1OLZ | X-ray | 2.0 | A | 24 | 649 |
| 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 |
| Q92854 | SEMA4D | Q92854-1 | Q92854-2 | 862 | 738 | 555 | 738 | Substitution | DKSKGSYRQHFFKHGGTAELKCSQKSNLARVFWKFQNGVLKAESPKYGLMGRKNLLIFNLSEGDSGVYQCLSEERVKNKTVFQVVAKHVLEVKVVPKPVVAPTLSVVQTEGSRIATKVLVASTQGSSPPTPAVQATSSGAITLPPKPAPTGTSCEPKIVINTVPQLHSEKTMYLKSSDNRLLMS | ASSPKPLPPPGSSSLSCLGHVGDRRLSSPWTPWPASGAGPDSSSRVSLLPPFLSDQAQHVHALGNFYLFCQATGPADIRFVWEKNGRALETCVPVQTHALPDGRAHALSWLQDAIRESAEYRCSVLSSAGNKTSKVQVAVMRPEVTHQERWTRELSAWRAVAGEHDRMMQSWRKAWESCSKDTL | 555 | 738 |
| Q92854 | SEMA4D | Q92854-1 | Q92854-2 | 862 | 738 | 739 | 862 | Deletion | none | none | 738 | 738 |
| Multiple sequence alignment of our canonical and alternatively spliced SEMA4D |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SEMA4D |
| UniProt-id | ENSG | ENST | ENSP |
| Q92854-1 | ENSG00000187764.12 | ENST00000356444.6 | ENSP00000348822.2 |
| Q92854-1 | ENSG00000187764.12 | ENST00000422704.7 | ENSP00000388768.2 |
| Q92854-1 | ENSG00000187764.12 | ENST00000438547.6 | ENSP00000405102.2 |
| Q92854-1 | ENSG00000187764.12 | ENST00000450295.5 | ENSP00000416523.1 |
| Q92854-2 | ENSG00000187764.12 | ENST00000339861.8 | ENSP00000344923.4 |
| Q92854-2 | ENSG00000187764.12 | ENST00000420987.5 | ENSP00000391733.1 |
| Q92854-2 | ENSG00000187764.12 | ENST00000455551.6 | ENSP00000411981.2 |
| UniProt-id | NM ID | NP ID |
| Q92854-1 | NM_006378.3 | NP_006369.3 |
| Q92854-1 | XM_011518123.2 | XP_011516425.1 |
| Q92854-1 | XM_011518124.2 | XP_011516426.1 |
| Q92854-1 | XM_011518125.1 | XP_011516427.1 |
| Q92854-1 | XM_011518127.2 | XP_011516429.1 |
| Q92854-1 | XM_011518128.2 | XP_011516430.1 |
| Q92854-1 | XM_011518129.1 | XP_011516431.1 |
| Q92854-1 | XM_011518130.2 | XP_011516432.1 |
| Q92854-1 | XM_011518131.2 | XP_011516433.1 |
| Q92854-1 | XM_011518133.2 | XP_011516435.1 |
| Q92854-1 | XM_011518134.2 | XP_011516436.1 |
| Q92854-1 | XM_017014193.1 | XP_016869682.1 |
| Q92854-1 | XM_017014194.1 | XP_016869683.1 |
| Q92854-1 | XM_017014195.1 | XP_016869684.1 |
| Q92854-1 | XM_017014198.1 | XP_016869687.1 |
| Q92854-2 | NM_001142287.1 | NP_001135759.1 |
| Amino acid sequences of our canonical and alternatively spliced SEMA4D |
| accession_id | Protein sequence |
| Q92854-1 | MRMCTPIRGLLMALAVMFGTAMAFAPIPRITWEHREVHLVQFHEPDIYNYSALLLSEDKDTLYIGAREAVFAVNALNISEKQHEVYWKVS EDKKAKCAEKGKSKQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDGELYSGTSYN FLGSEPIISRNSSHSPLRTEYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKK WTSFLKARLICSRPDSGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQSHTKWVRYNG PVPKPRPGACIDSEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHK AISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFVYAGSNSGVVQAPLAFCGKHGTCEDCVLARDPYCAWSPPTATCVALHQTESPSR GLIQEMSGDASVCPDKSKGSYRQHFFKHGGTAELKCSQKSNLARVFWKFQNGVLKAESPKYGLMGRKNLLIFNLSEGDSGVYQCLSEERV KNKTVFQVVAKHVLEVKVVPKPVVAPTLSVVQTEGSRIATKVLVASTQGSSPPTPAVQATSSGAITLPPKPAPTGTSCEPKIVINTVPQL HSEKTMYLKSSDNRLLMSLFLFFFVLFLCLFFYNCYKGYLPRQCLKFRSALLIGKKKPKSDFCDREQSLKETLVEPGSFSQQNGEHPKPA |
| Q92854-2 | MRMCTPIRGLLMALAVMFGTAMAFAPIPRITWEHREVHLVQFHEPDIYNYSALLLSEDKDTLYIGAREAVFAVNALNISEKQHEVYWKVS EDKKAKCAEKGKSKQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDGELYSGTSYN FLGSEPIISRNSSHSPLRTEYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKK WTSFLKARLICSRPDSGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQSHTKWVRYNG PVPKPRPGACIDSEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHK AISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFVYAGSNSGVVQAPLAFCGKHGTCEDCVLARDPYCAWSPPTATCVALHQTESPSR GLIQEMSGDASVCPASSPKPLPPPGSSSLSCLGHVGDRRLSSPWTPWPASGAGPDSSSRVSLLPPFLSDQAQHVHALGNFYLFCQATGPA DIRFVWEKNGRALETCVPVQTHALPDGRAHALSWLQDAIRESAEYRCSVLSSAGNKTSKVQVAVMRPEVTHQERWTRELSAWRAVAGEHD |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| SEMA4D (go to UniProt):Q92854 |
| 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 * 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 |
| Q92854 | Topological domain | 22 | 734 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=555;End=738 |
| Q92854 | Transmembrane | 735 | 755 | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=555;End=738 |
| Q92854 | Transmembrane | 735 | 755 | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=739;End=862 |
| Q92854 | Topological domain | 756 | 862 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=739;End=862 |
| Q92854 | Domain | 554 | 636 | Note=Ig-like C2-type | Type=Substitution;Start=555;End=738 |
| Q92854 | Region | 794 | 837 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=739;End=862 |
| Q92854 | Compositional bias | 823 | 837 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=739;End=862 |
Gene Isoform Structures and Expression Levels for SEMA4D |
| Gene structures of our canonical and alternative spliced genes of SEMA4D * 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 Q92854-1 |
| 3D view using mol* of Q92854-2 |
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 Q92854-1 |
 |
| pLDDT distribution across the protein length of Q92854-2 |
 |
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 Q92854-1 |
 |
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 |
| Q92854-1 | 1.027 | 101 | 1.033 | 247.989 | 0.545 | 0.739 | 0.982 | 0.506 | 1.074 | 0.471 | 0.692 | 29,30,32,505,506,507,508,511,514,515,557,559,560,5 62,575,576,577,578,579,580,583,626,628,637,638,639 ,640,641,642 |
| Q92854-2 | 1.029 | 248 | 1.059 | 1108.576 | 0.649 | 0.716 | 0.83 | 0.318 | 0.952 | 0.334 | 1.142 | 51,52,53,54,55,59,113,114,115,116,163,164,165,166, 167,210,211,212,213,214,215,236,292,293,294,295,29 6,297,298,299,300,301,302,303,419,420,421,422,423, 424,425,426,427,428,429,435,472,474,475,476,477,47 8,479,480,482,483,485,533,534 |
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 Q92854-1_Q92854-1_1olz_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q92854-1_1olz_A_Q92854-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q92854-1_Q92854-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q92854-1_vs_Q92854-2.png |
 < |
| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q92854-1_vs_Q92854-2.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 SEMA4D |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to SEMA4D |
| Previous studies relating to the alternative splicing of SEMA4D and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
Clinically important variants in SEMA4D |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
Copyright 2024-PresentThe University of Texas Health Science Center at Houston (UTHealth Houston) Web File Viewing | Emergency Information |