Human Gene CD2BP2 (ENST00000305596.8) from GENCODE V44
  Description: Homo sapiens CD2 cytoplasmic tail binding protein 2 (CD2BP2), transcript variant 1, mRNA. (from RefSeq NM_006110)
RefSeq Summary (NM_006110): This gene encodes a bi-functional protein. In the cytoplasm, the encoded protein binds the cytoplasmic tail of human surface antigen CD2 via its C-terminal GYF domain, and regulate CD2-triggered T lymphocyte activation. In the nucleus, this protein is a component of the U5 small nuclear ribonucleoprotein complex and is involved in RNA splicing. A pseudogene has been identified on chromosome 7. Alternative splicing results in multiple transcript variants but their biological validity has not been determined. [provided by RefSeq, Nov 2008].
Gencode Transcript: ENST00000305596.8
Gencode Gene: ENSG00000169217.9
Transcript (Including UTRs)
   Position: hg38 chr16:30,350,773-30,355,308 Size: 4,536 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr16:30,352,985-30,354,681 Size: 1,697 Coding Exon Count: 6 

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 (chr16:30,350,773-30,355,308)mRNA (may differ from genome)Protein (341 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD2B2_HUMAN
DESCRIPTION: RecName: Full=CD2 antigen cytoplasmic tail-binding protein 2; Short=CD2 cytoplasmic domain-binding protein 2; Short=CD2 tail-binding protein 2;
SUBUNIT: Binds the cytoplasmic domain of CD2 through the GYF domain.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Contains 1 GYF domain.

-  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: 31.18 RPKM in Spleen
Total median expression: 1052.05 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 -29.80123-0.242 Picture PostScript Text
3' UTR -879.702212-0.398 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
IPR003169 - GYF

Pfam Domains:
PF02213 - GYF domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1GYF - NMR MuPIT 1L2Z - NMR MuPIT 1SYX - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95400
FrontTopSide
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:0005515 protein binding
GO:0043021 ribonucleoprotein complex binding

Biological Process:
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0010923 negative regulation of phosphatase activity

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005682 U5 snRNP
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0046540 U4/U6 x U5 tri-snRNP complex


-  Descriptions from all associated GenBank mRNAs
  BC106082 - Homo sapiens cDNA clone IMAGE:4347332.
AB033004 - Homo sapiens mRNA for KIAA1178 protein, partial cds.
JD023552 - Sequence 4576 from Patent EP1572962.
JD035588 - Sequence 16612 from Patent EP1572962.
DQ590649 - Homo sapiens piRNA piR-57761, complete sequence.
LF205318 - JP 2014500723-A/12821: Polycomb-Associated Non-Coding RNAs.
MA440895 - JP 2018138019-A/12821: Polycomb-Associated Non-Coding RNAs.
AF109192 - Homo sapiens FWP010 mRNA, complete cds.
BC013854 - Homo sapiens CD2 (cytoplasmic tail) binding protein 2, mRNA (cDNA clone IMAGE:3447169).
BC000495 - Homo sapiens CD2 (cytoplasmic tail) binding protein 2, mRNA (cDNA clone MGC:8401 IMAGE:2820690), complete cds.
BC001947 - Homo sapiens CD2 (cytoplasmic tail) binding protein 2, mRNA (cDNA clone MGC:4324 IMAGE:2820690), complete cds.
AF104222 - Homo sapiens CD2 cytoplasmic domain binding protein (CD2BP2) mRNA, complete cds.
JD074499 - Sequence 55523 from Patent EP1572962.
JD178902 - Sequence 159926 from Patent EP1572962.
JD278117 - Sequence 259141 from Patent EP1572962.
JD167250 - Sequence 148274 from Patent EP1572962.
AK315708 - Homo sapiens cDNA, FLJ96807, Homo sapiens CD2 antigen (cytoplasmic tail) binding protein 2(CD2BP2), mRNA.
KJ893029 - Synthetic construct Homo sapiens clone ccsbBroadEn_02423 CD2BP2 gene, encodes complete protein.
DQ893574 - Synthetic construct clone IMAGE:100006204; FLH176220.01X; RZPDo839A11122D CD2 (cytoplasmic tail) binding protein 2 (CD2BP2) gene, encodes complete protein.
EU176630 - Synthetic construct Homo sapiens clone IMAGE:100011394; FLH176216.01L; RZPDo839A11121D CD2 (cytoplasmic tail) binding protein 2 (CD2BP2) gene, encodes complete protein.
KU178518 - Homo sapiens CD2 binding protein 2 isoform 1 (CD2BP2) mRNA, partial cds.
KU178519 - Homo sapiens CD2 binding protein 2 isoform 2 (CD2BP2) mRNA, partial cds, alternatively spliced.
LF319187 - JP 2014500723-A/126690: Polycomb-Associated Non-Coding RNAs.
MA554764 - JP 2018138019-A/126690: Polycomb-Associated Non-Coding RNAs.
DQ584102 - Homo sapiens piRNA piR-51214, complete sequence.
JD270792 - Sequence 251816 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95400 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDX2, CD2B2_HUMAN, ENST00000305596.1, ENST00000305596.2, ENST00000305596.3, ENST00000305596.4, ENST00000305596.5, ENST00000305596.6, ENST00000305596.7, KIAA1178, NM_006110, O95400, Q9ULP2, uc002dxs.1, uc002dxs.2, uc002dxs.3, uc002dxs.4
UCSC ID: ENST00000305596.8
RefSeq Accession: NM_006110
Protein: O95400 (aka CD2B2_HUMAN or C2B2_HUMAN)
CCDS: CCDS10675.1

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