Human Gene SEMA4B (ENST00000332496.10) from GENCODE V44
  Description: Homo sapiens semaphorin 4B (SEMA4B), transcript variant 1, mRNA. (from RefSeq NM_020210)
Gencode Transcript: ENST00000332496.10
Gencode Gene: ENSG00000185033.15
Transcript (Including UTRs)
   Position: hg38 chr15:90,184,963-90,229,670 Size: 44,708 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg38 chr15:90,201,579-90,228,643 Size: 27,065 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:90,184,963-90,229,670)mRNA (may differ from genome)Protein (837 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SEM4B_HUMAN
DESCRIPTION: RecName: Full=Semaphorin-4B; Flags: Precursor;
FUNCTION: Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
SIMILARITY: Belongs to the semaphorin family.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SIMILARITY: Contains 1 PSI domain.
SIMILARITY: Contains 1 Sema domain.
SEQUENCE CAUTION: Sequence=AAQ88758.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAR15707.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAB15372.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB21836.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 64.26 RPKM in Esophagus - Mucosa
Total median expression: 874.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -134.50240-0.560 Picture PostScript Text
3' UTR -347.601027-0.338 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR002165 - Plexin_repeat
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF01437 - Plexin repeat
PF01403 - Sema domain

ModBase Predicted Comparative 3D Structure on Q9NPR2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0038191 neuropilin binding

Biological Process:
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0030154 cell differentiation
GO:0050919 negative chemotaxis

Cellular Component:
GO:0005615 extracellular space
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK289991 - Homo sapiens cDNA FLJ77268 complete cds, highly similar to Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B (SEMA4B), transcript variant 1, mRNA.
AY358392 - Homo sapiens clone DNA67962 semaphorin C (UNQ749) mRNA, complete cds.
AY445887 - Homo sapiens semaphorin 4b precursor (SEMA4B) mRNA, complete cds.
AB051532 - Homo sapiens KIAA1745 mRNA for KIAA1745 protein.
BC126438 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone MGC:161716 IMAGE:8992154), complete cds.
BC144141 - Homo sapiens cDNA clone IMAGE:9052661.
JD458044 - Sequence 439068 from Patent EP1572962.
JD443220 - Sequence 424244 from Patent EP1572962.
JD227755 - Sequence 208779 from Patent EP1572962.
JD418496 - Sequence 399520 from Patent EP1572962.
BC110853 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone MGC:131831 IMAGE:6020867), complete cds.
AB385501 - Synthetic construct DNA, clone: pF1KA1745, Homo sapiens SEMA4B gene for semaphorin-4B precursor, complete cds, without stop codon, in Flexi system.
HQ258520 - Synthetic construct Homo sapiens clone IMAGE:100072949 sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B (SEMA4B), tra> (SEMA4B) gene, encodes complete protein.
KJ898229 - Synthetic construct Homo sapiens clone ccsbBroadEn_07623 SEMA4B gene, encodes complete protein.
KJ898230 - Synthetic construct Homo sapiens clone ccsbBroadEn_07624 SEMA4B gene, encodes complete protein.
AK026108 - Homo sapiens cDNA: FLJ22455 fis, clone HRC09777.
BX537671 - Homo sapiens mRNA; cDNA DKFZp686A04130 (from clone DKFZp686A04130).
AL390081 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1955967.
AK026133 - Homo sapiens cDNA: FLJ22480 fis, clone HRC10841.
BC010701 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone IMAGE:3855397), partial cds.
BC094849 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone IMAGE:4866983), partial cds.
JD137441 - Sequence 118465 from Patent EP1572962.
JD373565 - Sequence 354589 from Patent EP1572962.
JD468232 - Sequence 449256 from Patent EP1572962.
KJ906046 - Synthetic construct Homo sapiens clone ccsbBroadEn_15716 SEMA4B gene, encodes complete protein.
BC017658 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone IMAGE:3905299), partial cds.
AF258561 - Homo sapiens PP3686 mRNA, complete cds.
AK027083 - Homo sapiens cDNA: FLJ23430 fis, clone HRC11866.
BC019013 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B, mRNA (cDNA clone IMAGE:4562751).
AL390082 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 68748.
AL390080 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 159523.
JD495621 - Sequence 476645 from Patent EP1572962.
JD163346 - Sequence 144370 from Patent EP1572962.
JD442639 - Sequence 423663 from Patent EP1572962.
JD234801 - Sequence 215825 from Patent EP1572962.
JD434512 - Sequence 415536 from Patent EP1572962.
JD088122 - Sequence 69146 from Patent EP1572962.
JD088123 - Sequence 69147 from Patent EP1572962.
JD057767 - Sequence 38791 from Patent EP1572962.
JD407848 - Sequence 388872 from Patent EP1572962.
JD479910 - Sequence 460934 from Patent EP1572962.
JD378755 - Sequence 359779 from Patent EP1572962.
JD220381 - Sequence 201405 from Patent EP1572962.
JD369239 - Sequence 350263 from Patent EP1572962.
JD287988 - Sequence 269012 from Patent EP1572962.
JD321588 - Sequence 302612 from Patent EP1572962.
JD146393 - Sequence 127417 from Patent EP1572962.
JD060153 - Sequence 41177 from Patent EP1572962.
JD142308 - Sequence 123332 from Patent EP1572962.
JD470441 - Sequence 451465 from Patent EP1572962.
JD398316 - Sequence 379340 from Patent EP1572962.
JD055384 - Sequence 36408 from Patent EP1572962.
JD121553 - Sequence 102577 from Patent EP1572962.
JD059683 - Sequence 40707 from Patent EP1572962.
JD525437 - Sequence 506461 from Patent EP1572962.
JD079709 - Sequence 60733 from Patent EP1572962.
JD055509 - Sequence 36533 from Patent EP1572962.
JD316247 - Sequence 297271 from Patent EP1572962.
JD451130 - Sequence 432154 from Patent EP1572962.
JD077305 - Sequence 58329 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000332496.1, ENST00000332496.2, ENST00000332496.3, ENST00000332496.4, ENST00000332496.5, ENST00000332496.6, ENST00000332496.7, ENST00000332496.8, ENST00000332496.9, KIAA1745, NM_020210, Q6UXE3, Q8WVP9, Q96FK5, Q9C0B8, Q9H691, Q9NPM8, Q9NPN0, Q9NPR2, SEM4B_HUMAN, SEMAC, uc002boy.1, uc002boy.2, uc002boy.3, uc002boy.4, UNQ749/PRO1480
UCSC ID: ENST00000332496.10
RefSeq Accession: NM_020210
Protein: Q9NPR2 (aka SEM4B_HUMAN or SM4B_HUMAN)
CCDS: CCDS45347.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.