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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CSN1S2AP Gene

pseudogene   GIFtS: 27
GCID: GC04P070935

casein alpha s2-like A, pseudogene

(Previous name: casein alpha s2-like A )
(Previous symbol: CSN1S2A)
  Search for CSN1S2AP
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Biological research products
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Aliases
for CSN1S2AP gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Casein Alpha S2-Like A, Pseudogene1 2
CSN1S2A1 2
Casein Alpha S2-Like A1

External Ids:    HGNC: 202301   Entrez Gene: 2868282   Ensembl: ENSG000002341247   
ORGUL members:         
NONCODE:n406267    

Export aliases for CSN1S2AP gene to outside databases

Previous GC identifer: GC04P070934


Summaries
for CSN1S2AP gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for CSN1S2AP:
This locus is the equivalent of casein gamma in mouse (GeneID 12993) and is found in a cluster of casein genes, similar
to other mammals. In human, the potential open reading frame that matches the homologous protein from other species is
prematurely truncated shortly after the signal peptide. Therefore, this locus appears to be a pseudogene. (provided by
RefSeq, Jul 2008)




Genomic Views
for CSN1S2AP gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_022778.16  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for CSN1S2AP
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CSN1S2AP


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q13.3   Ensembl cytogenetic band:  4q13.3   HGNC cytogenetic band: 4q13.3

CSN1S2AP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CSN1S2AP gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P070935:  view genomic region     (about GC identifiers)

Start:
 70,933,103 bp from pter      End:
 70,951,007 bp from pter
Size:
 17,905 bases      Orientation:
 plus strand

Proteins
for CSN1S2AP gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for CSN1S2AP gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for CSN1S2AP gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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2 GenomeRNAi human phenotypes for CSN1S2AP:
 Decreased viability with pacli  Synthetic lethal with c-Myc af 


Pathways & Interactions
for CSN1S2AP gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CSN1S2AP

Drugs & Compounds
for CSN1S2AP gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for CSN1S2AP
Search CenterWatch for drugs/clinical trials and news about CSN1S2AP 

Transcripts
for CSN1S2AP gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for CSN1S2AP:

Casein alpha s2-like A, pseudogene
Hs.631945
Unigene Representative Sequence: NR_003720
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000451783(uc011car.2 uc003hez.3) ENST00000503813 ENST00000503711
ENST00000512167

miRNA
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Inhib. RNA
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Clone
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Primer
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Additional cDNA sequence: 

AY154892.1 BC128170.1 BC128173.1 BC141914.1 BC150502.1 NR_003720.1 

1 DOTS entry:

DT.121249457 

3 AceView cDNA sequences:

AY154892 BX485462 BX485461 

GeneLoc Exon Structure


Expression
for CSN1S2AP gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CSN1S2AP expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AGATAAAGCA

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image

CSN1S2AP expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
2 LifeMap In Vivo Development Anatomical Compartments/Cells 
Tissue Anatomical Compartment CellCategory (developmental path)
Skeletal MuscleHyoid Arch MusclesMononuclear MyocytesSkeletal Muscle
Skeletal MuscleMandibular Arch MusclesMononuclear MyocytesSkeletal Muscle
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

Genevestigator expression for CSN1S2AP

SOURCE GeneReport for Unigene cluster: Hs.631945
    SABiosciences Custom PCR Arrays for CSN1S2AP
Primer
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In Situ
Assay Products: 
 		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CSN1S2AP

Orthologs
for CSN1S2AP gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
This gene was present in the common ancestor of human and mouse.

Orthologs for CSN1S2AP gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Csn1s2a5 casein alpha s2-like A   --   5 (43.56 cM) 87774567 


ENSEMBL Gene Tree for CSN1S2AP (if available)
TreeFam Gene Tree for CSN1S2AP (if available) 

Paralogs
for CSN1S2AP gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for CSN1S2AP gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
SABiosciences Cancer Mutation PCR Assays
QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CSN1S2AP
DNA2.0 Custom Variant and Variant Library Synthesis for CSN1S2AP

Disorders / Diseases
for CSN1S2AP gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
   --

Publications
for CSN1S2AP gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for CSN1S2AP gene integrated from 9 sources:
(articles sorted by number of sources associating them with CSN1S2AP)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. (PubMed id 13679022)1, 3 Rijnkels M.... Rosen J.M. (2003)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
  3. Multispecies comparison of the casein gene loci and e volution of casein gene family. (PubMed id 12751895)1 Rijnkels M. (2002)

External Searches for CSN1S2AP gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing CSN1S2AP gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 286828 HGNC: 20230 AceView: CSN1S2A Ensembl:ENSG00000234124 euGenes: HUgn286828
ECgene: CSN1S2AP H-InvDB: CSN1S2AP

Other Databases showing CSN1S2AP gene

(According to HUGE)
About This Section
   --

Specialized Databases showing CSN1S2AP gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for CSN1S2AP Pharmacogenomics, SNPs, Pathways

Intellectual Property
for CSN1S2AP gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for CSN1S2AP gene:
Search GeneIP for patents involving CSN1S2AP

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
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