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

SRRM4 Gene

protein-coding   GIFtS: 45
GCID: GC12P119420

serine/arginine repetitive matrix 4

(Previous name: KIAA1853 )
(Previous symbol: KIAA1853)
 Explore 7 diseases affiliated with
SRRM4 via our new
 Human Malady Compendium 
Biological research products
for SRRM4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Serine/Arginine Repetitive Matrix 41 2     Neural-Specific SR-Related Protein Of 100 KDa2 3
KIAA18531 2 3 5     MU-MB-2.762
NSR1005     Serine/Arginine Repetitive Matrix Protein 42
Medulloblastoma Antigen MU-MB-2.762 3     NSR1005
Neural-Specific Serine/Arginine Repetitive Splicing Factor Of 100 KDa2 3     

External Ids:    HGNC: 293891   Entrez Gene: 845302   Ensembl: ENSG000001397677   OMIM: 6131035   UniProtKB: A7MD483   

Export aliases for SRRM4 gene to outside databases

Previous GC identifers: GC12P117903 GC12P116428


(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 SRRM4:
SRRM4 promotes alternative splicing and inclusion of neural-specific exons in target mRNAs (Calarco et al., 2009
(PubMed 19737518)).(supplied by OMIM, Oct 2009)

UniProtKB/Swiss-Prot: SRRM4_HUMAN, A7MD48
Function: Splicing factor specifically required for neural cell differentiation. Acts in conjuction with nPTB/PTBP2 by
binding directly to its regulated target transcripts and promotes neural-specific exon inclusion in many genes that
function in neural cell differentiation. Required to promote the inclusion of neural-specific exon 10 in nPTB/PTBP2,
leading to increased expression of neural-specific nPTB/PTBP2. Also promotes the inclusion of exon 16 in DAAM1 in
neuron extracts (By similarity)




(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_000012.11  NC_018923.1  NT_009775.17  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SRRM4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SRRM4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SRRM4


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

Entrez Gene cytogenetic band: 12q24.23   Ensembl cytogenetic band:  12q24.23   HGNC cytogenetic band: 12q24.23

SRRM4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SRRM4 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P119420:  view genomic region     (about GC identifiers)

Start:
119,419,300 bp from pter      End:
119,600,857 bp from pter
Size:
181,558 bases      Orientation:
plus strand

(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/Swiss-Prot: SRRM4_HUMAN, A7MD48 (See protein sequence)
Recommended Name: Serine/arginine repetitive matrix protein 4  
Size: 611 amino acids; 68559 Da
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=BAB47482.1; Type=Erroneous initiation;
Secondary accessions: A8K5P6 B2RZH7 Q7Z5F0 Q96JH4

Explore the universe of human proteins at neXtProt for SRRM4: NX_A7MD48

Post-translational modifications:

  • Phosphorylated (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A7MD48

  • SRRM4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_919262.2  
    ENSEMBL proteins: 
     ENSP00000267260  

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    Uscn Proteins for SRRM4

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--


    SRRM4 for ontologies           About GeneDecksing



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

    ProtoNet protein and cluster: A7MD48

    UniProtKB/Swiss-Prot: SRRM4_HUMAN, A7MD48
    Similarity: Belongs to the nSR100 family


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: SRRM4_HUMAN, A7MD48
    Function: Splicing factor specifically required for neural cell differentiation. Acts in conjuction with nPTB/PTBP2 by
    binding directly to its regulated target transcripts and promotes neural-specific exon inclusion in many genes that
    function in neural cell differentiation. Required to promote the inclusion of neural-specific exon 10 in nPTB/PTBP2,
    leading to increased expression of neural-specific nPTB/PTBP2. Also promotes the inclusion of exon 16 in DAAM1 in
    neuron extracts (By similarity)

    miRNA
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    hsa-miR-4254 hsa-miR-3194-5p hsa-miR-146a hsa-miR-134 hsa-miR-3921 hsa-miR-298 hsa-miR-149 hsa-miR-200b
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    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003729mRNA binding ISS--


    SRRM4 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for SRRM4:
     Decreased POU5F1-GFP protein e  Increased gamma-H2AX phosphory 


    (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 SRRM4

    1 Interacting protein for SRRM4 (A7MD483) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CACNA1AO005553I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing ISS--
    GO:0007399nervous system development ISS--
    GO:0008380RNA splicing IEA--
    GO:0030154cell differentiation ISS--
    GO:0043484regulation of RNA splicing ISS--


    SRRM4 for ontologies           About GeneDecksing



    (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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SRRM4
    Search CenterWatch for drugs/clinical trials and news about SRRM4 

    (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

    REFSEQ mRNAs for SRRM4 gene: 
    NM_194286.3  

    Unigene Cluster for SRRM4:

    Serine/arginine repetitive matrix 4
    Hs.112577  [show with all ESTs]
    Unigene Representative Sequence: NM_194286
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000267260(uc001txa.2) ENST00000545224 ENST00000537597

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SRRM4
    8/86 QIAGEN miScript miRNA Assays for microRNAs that regulate SRRM4 (see all 86):
    hsa-miR-4254 hsa-miR-3194-5p hsa-miR-146a hsa-miR-134 hsa-miR-3921 hsa-miR-298 hsa-miR-149 hsa-miR-200b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Browse for Gene Knock-down Tools from EMD Millipore
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    OriGene shRNA RFP: SRRM4
    OriGene siRNA: SRRM4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SRRM4
    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SRRM4
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    Additional cDNA sequence: 

    AB058756.1 AK055717.1 AK125400.1 AK291361.1 AY130006.1 BC152471.1 BC167162.1 BC167163.1 

    1 DOTS entry:

    DT.306671 

    24/64 AceView cDNA sequences (see all 64):

    BQ719476 AI701523 AB058756 AA324027 R12793 BX281343 NM_194286 BM672974 
    AA608629 BE218946 BX488955 BM723637 AI887860 F23308 AW594642 AL707158 
    BF062141 BM927278 R87586 AW962002 CA976031 BQ070814 BM686798 AW071669 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for SRRM4    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4
    SP1:                    -                     
    SP2:                    -                     
    SP3:                                          


    ECgene alternative splicing isoforms for SRRM4

    (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

    SRRM4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTATGGTGTT

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

    About this image

    SRRM4 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)
    BrainBlood Brain BarrierEndothelial CellsBlood Brain Barrier, Endothelium
    BoneMaxillary ProcessBone
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SRRM4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SRRM4

    SOURCE GeneReport for Unigene cluster: Hs.112577

    UniProtKB/Swiss-Prot: SRRM4_HUMAN, A7MD48
    Tissue specificity: Specifically expressed in neuronal cells (at protein level). Expressed in the cerebellum

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SRRM4

    (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 animals.

    Orthologs for SRRM4 gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SRRM41 serine/arginine repetitive matrix 4 68.19(n)
    64.97(a)
      416989  XM_415281.3  XP_415281.3 
    lizard
    (Anolis carolinensis)
    Reptilia SRRM46
    --
    47(a)
    1 ↔ 1
    GL343338.1(531384-577332)
    zebrafish
    (Danio rerio)
    Actinopterygii srrm41 serine/arginine repetitive matrix 4 47.69(n)
    44.4(a)
      796574  XM_001336887.2  XP_001336923.2 
    honey bee
    (Apis mellifera)
    Insecta --
    --
    9(a)
    possible ortholog
    GroupUn.1473(11966-15820)
    worm
    (Caenorhabditis elegans)
    Secernentea C15C6.36
    Protein C15C6.3
    8(a)
    1 ↔ 1
    I(12207086-12212197)


    ENSEMBL Gene Tree for SRRM4 (if available)
    TreeFam Gene Tree for SRRM4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SRRM4 gene
    SRRM32  SRRM22  SRRM12  C2orf162  SRRM52  

    SRRM4 for paralogs           About GeneDecksing



    (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

    10/3424 NCBI SNPs in SRRM4 are shown (see all 3424    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs108510581,2
    C,F,A,H,--119417341(+) GTTTTG/TCATAT 1 -- us2k1 tfbs39Minor allele frequency- T:0.10NS EA NA WA 542
    rs110692111,2
    C,F,A,H,--119417417(+) GTGGGG/AGTAGG 1 -- us2k18Minor allele frequency- A:0.12NS EA NA CSA 648
    rs1438227891,2
    --119417465(+) TACCCC/TAAATG 1 -- us2k10--------
    rs123095001,2
    C,F,A,H,--119417567(+) GGAAAC/TGGGGG 1 -- us2k110Minor allele frequency- T:0.24NS EA NA WA CSA 650
    rs761048181,2
    F,--119417707(+) TCCCCC/AGGCAA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1828310051,2
    --119417713(+) GGCAAC/GCCACA 1 -- us2k10--------
    rs1481372441,2
    --119417739(+) TGCACC/TTCTCG 1 -- us2k10--------
    rs1158032191,2
    F,--119417746(+) CTCGTT/CGTTGA 1 -- us2k11Minor allele frequency- C:0.02WA 118
    rs796975871,2
    C,F,--119417812(+) GCAGGC/TGTGTC 1 -- us2k11Minor allele frequency- T:0.05WA 118
    rs1419701361,2
    --119417845(+) GATACA/CCTTTG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SRRM4 (119419300 - 119600857 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SRRM4
         1 CNV: 1933

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    (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

    SRRM4 for disorders           About GeneDecksing

    OMIM gene information: 613103    OMIM disorders: --

    7 diseases for SRRM4:    About MalaCards
    medulloblastoma    large cell medulloblastoma    childhood medulloblastoma    macular degeneration
    ataxia    malaria    neuronitis

    Human Genome Epidemiology (HuGE) Navigator: SRRM4 (1 document)

    Export disorders for SRRM4 gene to outside databases

    (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 SRRM4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SRRM4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. (PubMed id 19737518)1, 2, 3 Calarco J.A.... Blencowe B.J. (2009)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PubMed id 12800201)1, 2 Behrends U.... Mautner J. (2003)
    4. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 11347906)1, 2 Nagase T.... Ohara O. (2001)
    5. Comparison of an expanded ataxia interactome with pat ient medical records reveals a relationship between macular degeneration and at axia. (PubMed id 21078624)1 Kahle J.J....Zoghbi H.Y. (2011)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    8. 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)
    9. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84530 HGNC: 29389 AceView: KIAA1853 Ensembl:ENSG00000139767 euGenes: HUgn84530
    ECgene: SRRM4 H-InvDB: SRRM4

    (According to HUGE)
    About This Section
    HUGE: KIAA1853

    (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 SRRM4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SRRM4 gene:
    Search GeneIP for patents involving SRRM4

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    VWF
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    von Willebrand factor
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    Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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