Human Gene BCAS2 (ENST00000369541.4_7) from GENCODE V47lift37
  Description: BCAS2 pre-mRNA processing factor (from RefSeq NM_005872.3)
Gencode Transcript: ENST00000369541.4_7
Gencode Gene: ENSG00000116752.6_9
Transcript (Including UTRs)
   Position: hg19 chr1:115,110,178-115,124,236 Size: 14,059 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:115,110,751-115,124,212 Size: 13,462 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:115,110,178-115,124,236)mRNA (may differ from genome)Protein (225 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPF27_HUMAN
DESCRIPTION: RecName: Full=Pre-mRNA-splicing factor SPF27; AltName: Full=Breast carcinoma-amplified sequence 2; AltName: Full=DNA amplified in mammary carcinoma 1 protein; AltName: Full=Spliceosome-associated protein SPF 27;
FUNCTION: Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. May have a scaffolding role in the spliceosome assembly as it contacts all other components of the core complex.
SUBUNIT: Component of the PRP19-CDC5L splicing complex composed of a core complex comprising a homotetramer of PRPF19, CDC5L, PLRG1 and BCAS2, and at least three less stably associated proteins CTNNBL1, CWC15 and HSPA8. Interacts directly in the complex with PRPF19, CDC5L and PLRG1.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the SPF27 family.

-  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

+  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: 36.47 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1075.28 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 -4.8024-0.200 Picture PostScript Text
3' UTR -111.80573-0.195 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
IPR008409 - BCAS2

Pfam Domains:
PF05700 - Breast carcinoma amplified sequence 2 (BCAS2)

SCOP Domains:
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on O75934
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0005813 centrosome
GO:0016607 nuclear speck
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071011 precatalytic spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:0005662 DNA replication factor A complex


-  Descriptions from all associated GenBank mRNAs
  DQ892529 - Synthetic construct clone IMAGE:100005159; FLH187201.01X; RZPDo839E1072D breast carcinoma amplified sequence 2 (BCAS2) gene, encodes complete protein.
BC063894 - Homo sapiens DENN/MADD domain containing 2C, mRNA (cDNA clone IMAGE:30389241).
BC039238 - Homo sapiens breast carcinoma amplified sequence 2, mRNA (cDNA clone IMAGE:4688387).
AK222637 - Homo sapiens mRNA for breast carcinoma amplified sequence 2 variant, clone: CBL04884.
BC022880 - Homo sapiens breast carcinoma amplified sequence 2, mRNA (cDNA clone MGC:27160 IMAGE:3930637), complete cds.
LF383821 - JP 2014500723-A/191324: Polycomb-Associated Non-Coding RNAs.
BC005285 - Homo sapiens breast carcinoma amplified sequence 2, mRNA (cDNA clone MGC:12341 IMAGE:3930559), complete cds.
AB020623 - Homo sapiens DAM1 mRNA, complete cds.
BC012623 - Homo sapiens breast carcinoma amplified sequence 2, mRNA (cDNA clone MGC:13667 IMAGE:4073772), complete cds.
JD249024 - Sequence 230048 from Patent EP1572962.
JD510202 - Sequence 491226 from Patent EP1572962.
JD552925 - Sequence 533949 from Patent EP1572962.
JD513237 - Sequence 494261 from Patent EP1572962.
JD284170 - Sequence 265194 from Patent EP1572962.
JD348853 - Sequence 329877 from Patent EP1572962.
LF352868 - JP 2014500723-A/160371: Polycomb-Associated Non-Coding RNAs.
JD090993 - Sequence 72017 from Patent EP1572962.
JD437327 - Sequence 418351 from Patent EP1572962.
LF352867 - JP 2014500723-A/160370: Polycomb-Associated Non-Coding RNAs.
JD296814 - Sequence 277838 from Patent EP1572962.
EU832613 - Synthetic construct Homo sapiens clone HAIB:100067642; DKFZo008A0831 breast carcinoma amplified sequence 2 protein (BCAS2) gene, encodes complete protein.
LF352866 - JP 2014500723-A/160369: Polycomb-Associated Non-Coding RNAs.
AF081788 - Homo sapiens putative spliceosome associated protein mRNA, complete cds.
CR542037 - Homo sapiens full open reading frame cDNA clone RZPDo834B0136D for gene BCAS2, breast carcinoma amplified sequence 2; complete cds, incl. stopcodon.
AK313141 - Homo sapiens cDNA, FLJ93631, Homo sapiens breast carcinoma amplified sequence 2 (BCAS2), mRNA.
EU176700 - Synthetic construct Homo sapiens clone IMAGE:100011497; FLH187200.01L; RZPDo839H05255D breast carcinoma amplified sequence 2 (BCAS2) gene, encodes complete protein.
EU832684 - Synthetic construct Homo sapiens clone HAIB:100067713; DKFZo004A0832 breast carcinoma amplified sequence 2 protein (BCAS2) gene, encodes complete protein.
KJ892991 - Synthetic construct Homo sapiens clone ccsbBroadEn_02385 BCAS2 gene, encodes complete protein.
AB451245 - Homo sapiens BCAS2 mRNA for breast carcinoma amplified sequence 2, complete cds, clone: FLJ08051AAAN.
BT019390 - Homo sapiens breast carcinoma amplified sequence 2 mRNA, complete cds.
AB451369 - Homo sapiens BCAS2 mRNA for breast carcinoma amplified sequence 2, partial cds, clone: FLJ08051AAAF.
AB528339 - Synthetic construct DNA, clone: pF1KB6916, Homo sapiens BCAS2 gene for breast carcinoma amplified sequence 2, without stop codon, in Flexi system.
LF352865 - JP 2014500723-A/160368: Polycomb-Associated Non-Coding RNAs.
CU675083 - Synthetic construct Homo sapiens gateway clone IMAGE:100020187 5' read BCAS2 mRNA.
LF352863 - JP 2014500723-A/160366: Polycomb-Associated Non-Coding RNAs.
LF352861 - JP 2014500723-A/160364: Polycomb-Associated Non-Coding RNAs.
MA619398 - JP 2018138019-A/191324: Polycomb-Associated Non-Coding RNAs.
MA588445 - JP 2018138019-A/160371: Polycomb-Associated Non-Coding RNAs.
MA588444 - JP 2018138019-A/160370: Polycomb-Associated Non-Coding RNAs.
MA588443 - JP 2018138019-A/160369: Polycomb-Associated Non-Coding RNAs.
MA588442 - JP 2018138019-A/160368: Polycomb-Associated Non-Coding RNAs.
MA588440 - JP 2018138019-A/160366: Polycomb-Associated Non-Coding RNAs.
MA588438 - JP 2018138019-A/160364: Polycomb-Associated Non-Coding RNAs.

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

Protein O75934 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) 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: DAM1 , ENST00000369541.1, ENST00000369541.2, ENST00000369541.3, NM_005872, O75934, Q6FGS0, SPF27_HUMAN, uc318hqq.1, uc318hqq.2
UCSC ID: ENST00000369541.4_7
RefSeq Accession: NM_005872.3
Protein: O75934 (aka SPF27_HUMAN)

-  Gene Model Information
  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.