Human Gene SEMA4G (uc010qpt.1)
  Description: Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G (SEMA4G), transcript variant 2, mRNA.
RefSeq Summary (NM_001203244): Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr10:102,729,290-102,740,739 Size: 11,450 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr10:102,732,670-102,740,737 Size: 8,068 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:102,729,290-102,740,739)mRNA (may differ from genome)Protein (542 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDHuman Cortex Gene ExpressionLynxMGI
neXtProtPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SEM4G_HUMAN
DESCRIPTION: RecName: Full=Semaphorin-4G; Flags: Precursor;
FUNCTION: Cell surface receptor for PLXNB2. May play a role in axon guidance (By similarity).
SUBUNIT: Interacts with PLXNB2 (By similarity).
SUBCELLULAR LOCATION: Cell 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=BAB13445.1; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SEMA4G
CDC HuGE Published Literature: SEMA4G

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.79 RPKM in Colon - Transverse
Total median expression: 146.38 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -133.14443-0.301 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR002165 - Plexin_repeat
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF01403 - Sema domain
PF01437 - Plexin repeat

SCOP Domains:
101912 - Sema domain
103575 - Plexin repeat

ModBase Predicted Comparative 3D Structure on Q9NTN9
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
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:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC051030 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G, mRNA (cDNA clone MGC:51988 IMAGE:5164957), complete cds.
AK297431 - Homo sapiens cDNA FLJ60700 complete cds, highly similar to Semaphorin-4G precursor.
JD188107 - Sequence 169131 from Patent EP1572962.
JD112791 - Sequence 93815 from Patent EP1572962.
JD086112 - Sequence 67136 from Patent EP1572962.
JD290570 - Sequence 271594 from Patent EP1572962.
BC128579 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G, mRNA (cDNA clone MGC:157728 IMAGE:40129134), complete cds.
JD420473 - Sequence 401497 from Patent EP1572962.
AB046839 - Homo sapiens KIAA1619 mRNA for KIAA1619 protein.
BC110382 - Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G, mRNA (cDNA clone MGC:102867 IMAGE:5163607), complete cds.
JD253078 - Sequence 234102 from Patent EP1572962.
AB463245 - Synthetic construct DNA, clone: pF1KA1619, Homo sapiens SEMA4G gene for sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G, without stop codon, in Flexi system.
KJ906283 - Synthetic construct Homo sapiens clone ccsbBroadEn_15953 SEMA4G gene, encodes complete protein.
JD485381 - Sequence 466405 from Patent EP1572962.
JD465602 - Sequence 446626 from Patent EP1572962.
JD271156 - Sequence 252180 from Patent EP1572962.
JD230867 - Sequence 211891 from Patent EP1572962.
CU691975 - Synthetic construct Homo sapiens gateway clone IMAGE:100021069 3' read MRPL43 mRNA.
JD207406 - Sequence 188430 from Patent EP1572962.
JD157848 - Sequence 138872 from Patent EP1572962.
JD338841 - Sequence 319865 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: A1A5C6, A6NJY8, AK297431, KIAA1619, NM_001203244, NP_001190173, Q58EY1, Q9HCF3, Q9NTN9, SEM4G_HUMAN
UCSC ID: uc010qpt.1
RefSeq Accession: NM_001203244
Protein: Q9NTN9 (aka SEM4G_HUMAN or SM4G_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK297431.1
exon count: 13CDS single in 3' UTR: no RNA size: 2655
ORF size: 1626CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 3171.50frame shift in genome: no % Coverage: 75.74
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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