Human Gene SIRPB2 (ENST00000359801.8) from GENCODE V44
  Description: Homo sapiens signal regulatory protein beta 2 (SIRPB2), transcript variant 1, mRNA. (from RefSeq NM_001122962)
Gencode Transcript: ENST00000359801.8
Gencode Gene: ENSG00000196209.13
Transcript (Including UTRs)
   Position: hg38 chr20:1,474,578-1,491,420 Size: 16,843 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr20:1,476,167-1,491,359 Size: 15,193 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:1,474,578-1,491,420)mRNA (may differ from genome)Protein (342 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMGIneXtProtPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIRB2_HUMAN
DESCRIPTION: RecName: Full=Signal-regulatory protein beta-2; Short=SIRP-beta-2; AltName: Full=Protein tyrosine phosphatase non-receptor type substrate 1-like 3; AltName: Full=Protein tyrosine phosphatase non-receptor type substrate protein; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
SIMILARITY: Contains 2 Ig-like V-type (immunoglobulin-like) domains.

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.64 RPKM in Whole Blood
Total median expression: 67.47 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 -15.5061-0.254 Picture PostScript Text
3' UTR -515.101589-0.324 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
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

ModBase Predicted Comparative 3D Structure on Q5JXA9
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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 Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK095499 - Homo sapiens cDNA FLJ38180 fis, clone FCBBF1000121, weakly similar to Homo sapiens mRNA for SHPS-1.
AK297072 - Homo sapiens cDNA FLJ59715 complete cds.
AK294440 - Homo sapiens cDNA FLJ52409 complete cds.
AY424277 - Homo sapiens protein tyrosine phosphatase non-receptor type substrate protein mRNA, complete cds, alternatively spliced.
JD133218 - Sequence 114242 from Patent EP1572962.
AK097113 - Homo sapiens cDNA FLJ39794 fis, clone SPLEN2003924, highly similar to HEAT SHOCK 70 KDA PROTEIN 1.
JD205752 - Sequence 186776 from Patent EP1572962.
JD186373 - Sequence 167397 from Patent EP1572962.
JD057851 - Sequence 38875 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000359801.1, ENST00000359801.2, ENST00000359801.3, ENST00000359801.4, ENST00000359801.5, ENST00000359801.6, ENST00000359801.7, NM_001122962, PTPN1L, PTPNS1L3, Q5JXA9, Q6TCH9, SIRB2_HUMAN, uc002wfg.1, uc002wfg.2, uc002wfg.3, uc002wfg.4
UCSC ID: ENST00000359801.8
RefSeq Accession: NM_001122962
Protein: Q5JXA9 (aka SIRB2_HUMAN or SRB2_HUMAN)
CCDS: CCDS42849.1

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