CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-018850
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Semaphorin-4D 
Protein Synonyms/Alias
 A8; BB18; GR3; CD100 
Gene Name
 SEMA4D 
Gene Synonyms/Alias
 C9orf164; CD100; SEMAJ 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
81NALNISEKQHEVYWKubiquitination[1]
104CAEKGKSKQTECLNYubiquitination[1]
148TSFKFLGKNEDGKGRubiquitination[1]
505APLAFCGKHGTCEDCubiquitination[1]
556DASVCPDKSKGSYRQubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961] 
Functional Description
 Cell surface receptor for PLXN1B and PLXNB2 that plays an important role in cell-cell signaling. Promotes reorganization of the actin cytoskeleton and plays a role in axonal growth cone guidance in the developing central nervous system. Regulates dendrite and axon branching and morphogenesis. Promotes the migration of cerebellar granule cells and of endothelial cells. Plays a role in the immune system; induces B-cells to aggregate and improves their viability (in vitro). Promotes signaling via SRC and PTK2B/PYK2, which then mediates activation of phosphatidylinositol 3-kinase and of the AKT1 signaling cascade. Interaction with PLXNB1 mediates activation of RHOA. 
Sequence Annotation
 DOMAIN 22 500 Sema.
 DOMAIN 502 551 PSI.
 DOMAIN 554 636 Ig-like C2-type.
 CARBOHYD 49 49 N-linked (GlcNAc...).
 CARBOHYD 74 74 N-linked (GlcNAc...); atypical.
 CARBOHYD 77 77 N-linked (GlcNAc...).
 CARBOHYD 139 139 N-linked (GlcNAc...).
 CARBOHYD 191 191 N-linked (GlcNAc...).
 CARBOHYD 329 329 N-linked (GlcNAc...).
 CARBOHYD 379 379 N-linked (GlcNAc...).
 CARBOHYD 419 419 N-linked (GlcNAc...).
 CARBOHYD 613 613 N-linked (GlcNAc...) (Potential).
 CARBOHYD 632 632 N-linked (GlcNAc...) (Potential).
 DISULFID 97 108
 DISULFID 126 135
 DISULFID 257 370
 DISULFID 281 326
 DISULFID 503 520
 DISULFID 509 553
 DISULFID 512 529
 DISULFID 576 624  
Keyword
 3D-structure; Alternative splicing; Cell membrane; Complete proteome; Developmental protein; Differentiation; Disulfide bond; Glycoprotein; Immunoglobulin domain; Membrane; Neurogenesis; Polymorphism; Receptor; Reference proteome; Signal; Transmembrane; Transmembrane helix. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 862 AA 
Protein Sequence
MRMCTPIRGL LMALAVMFGT AMAFAPIPRI TWEHREVHLV QFHEPDIYNY SALLLSEDKD 60
TLYIGAREAV FAVNALNISE KQHEVYWKVS EDKKAKCAEK GKSKQTECLN YIRVLQPLSA 120
TSLYVCGTNA FQPACDHLNL TSFKFLGKNE DGKGRCPFDP AHSYTSVMVD GELYSGTSYN 180
FLGSEPIISR NSSHSPLRTE YAIPWLNEPS FVFADVIRKS PDSPDGEDDR VYFFFTEVSV 240
EYEFVFRVLI PRIARVCKGD QGGLRTLQKK WTSFLKARLI CSRPDSGLVF NVLRDVFVLR 300
SPGLKVPVFY ALFTPQLNNV GLSAVCAYNL STAEEVFSHG KYMQSTTVEQ SHTKWVRYNG 360
PVPKPRPGAC IDSEARAANY TSSLNLPDKT LQFVKDHPLM DDSVTPIDNR PRLIKKDVNY 420
TQIVVDRTQA LDGTVYDVMF VSTDRGALHK AISLEHAVHI IEETQLFQDF EPVQTLLLSS 480
KKGNRFVYAG SNSGVVQAPL AFCGKHGTCE DCVLARDPYC AWSPPTATCV ALHQTESPSR 540
GLIQEMSGDA SVCPDKSKGS YRQHFFKHGG TAELKCSQKS NLARVFWKFQ NGVLKAESPK 600
YGLMGRKNLL IFNLSEGDSG VYQCLSEERV KNKTVFQVVA KHVLEVKVVP KPVVAPTLSV 660
VQTEGSRIAT KVLVASTQGS SPPTPAVQAT SSGAITLPPK PAPTGTSCEP KIVINTVPQL 720
HSEKTMYLKS SDNRLLMSLF LFFFVLFLCL FFYNCYKGYL PRQCLKFRSA LLIGKKKPKS 780
DFCDREQSLK ETLVEPGSFS QQNGEHPKPA LDTGYETEQD TITSKVPTDR EDSQRIDDLS 840
ARDKPFDVKC ELKFADSDAD GD 862 
Gene Ontology
 GO:0005615; C:extracellular space; ISS:BHF-UCL.
 GO:0005887; C:integral to plasma membrane; IDA:UniProtKB.
 GO:0030215; F:semaphorin receptor binding; ISS:BHF-UCL.
 GO:0004888; F:transmembrane signaling receptor activity; IMP:UniProtKB.
 GO:0007411; P:axon guidance; TAS:Reactome.
 GO:0006955; P:immune response; TAS:ProtInc.
 GO:0070486; P:leukocyte aggregation; IMP:UniProtKB.
 GO:0010693; P:negative regulation of alkaline phosphatase activity; IMP:BHF-UCL.
 GO:0043066; P:negative regulation of apoptotic process; TAS:ProtInc.
 GO:0045668; P:negative regulation of osteoblast differentiation; ISS:BHF-UCL.
 GO:0050732; P:negative regulation of peptidyl-tyrosine phosphorylation; ISS:BHF-UCL.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:BHF-UCL.
 GO:0043931; P:ossification involved in bone maturation; IMP:BHF-UCL.
 GO:0030335; P:positive regulation of cell migration; IDA:UniProtKB.
 GO:0048672; P:positive regulation of collateral sprouting; IMP:UniProtKB.
 GO:0050731; P:positive regulation of peptidyl-tyrosine phosphorylation; ISS:BHF-UCL.
 GO:0014068; P:positive regulation of phosphatidylinositol 3-kinase cascade; IMP:UniProtKB.
 GO:0032321; P:positive regulation of Rho GTPase activity; IMP:UniProtKB.
 GO:0008360; P:regulation of cell shape; IMP:UniProtKB.
 GO:0048814; P:regulation of dendrite morphogenesis; IMP:UniProtKB.
 GO:1900220; P:semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis; ISS:BHF-UCL. 
Interpro
 IPR007110; Ig-like_dom.
 IPR013783; Ig-like_fold.
 IPR003599; Ig_sub.
 IPR013151; Immunoglobulin.
 IPR003659; Plexin-like.
 IPR016201; Plexin-like_fold.
 IPR002165; Plexin_repeat.
 IPR027231; Semaphorin.
 IPR001627; Semaphorin/CD100_Ag.
 IPR015943; WD40/YVTN_repeat-like_dom. 
Pfam
 PF00047; ig
 PF01437; PSI
 PF01403; Sema 
SMART
 SM00409; IG
 SM00423; PSI
 SM00630; Sema 
PROSITE
 PS50835; IG_LIKE
 PS51004; SEMA 
PRINTS