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

Aliases for SRRM4 Gene

Aliases for SRRM4 Gene

  • Serine/Arginine Repetitive Matrix 4 2 3 5
  • Neural-Specific SR-Related Protein Of 100 KDa 2 3 4
  • KIAA1853 2 3 4
  • NSR100 2 3 4
  • Neural-Specific Serine/Arginine Repetitive Splicing Factor Of 100 KDa 3 4
  • Serine/Arginine Repetitive Matrix Protein 4 3 4
  • Medulloblastoma Antigen MU-MB-2.76 3 4
  • MU-MB-2.76 3
  • SRRM4 5

External Ids for SRRM4 Gene

Previous HGNC Symbols for SRRM4 Gene

  • KIAA1853

Previous GeneCards Identifiers for SRRM4 Gene

  • GC12P117903
  • GC12P119420
  • GC12P116428

Summaries for SRRM4 Gene

Entrez Gene Summary for SRRM4 Gene

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

GeneCards Summary for SRRM4 Gene

SRRM4 (Serine/Arginine Repetitive Matrix 4) is a Protein Coding gene. Diseases associated with SRRM4 include Deafness, Autosomal Dominant 27 and Medulloblastoma. Gene Ontology (GO) annotations related to this gene include mRNA binding.

UniProtKB/Swiss-Prot Summary for SRRM4 Gene

  • Splicing factor specifically required for neural cell differentiation. Acts in conjunction 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). Promotes alternative splicing of REST transcripts to produce REST isoform 3 (REST4) with greatly reduced repressive activity, thereby activating expression of REST targets in neural cells (PubMed:30684677). Plays an important role during embryonic development as well as in the proper functioning of the adult nervous system. Regulates alternative splicing events in genes with important neuronal functions (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SRRM4 Gene

Genomics for SRRM4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SRRM4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J118979 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 600.7 -0.5 -500 2.3 CTCF TEAD4 REST POLR2A RAD21 NRF1 ZNF444 SMC3 YY1 MIER1 SRRM4 lnc-TAOK3-13 SUDS3
GH12J118287 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.4 -693.3 -693340 1.6 LEF1 IKZF1 JUND DPF2 HDAC1 SOX6 GATAD2B EP300 SCRT2 THRA SUDS3 TAOK3 SRRM4 ENSG00000213144 RF00017-1299 HE856110 lnc-VSIG10-4 PEBP1
GH12J119006 Enhancer 0.8 Ensembl ENCODE CraniofacialAtlas 11.9 +24.6 24637 2.3 KDM1A POLR2A RCOR1 SMARCA4 ZNF652 GATA2 SRRM4 piR-49645-001 piR-38351-119 HSPB8
GH12J119008 Enhancer 0.8 ENCODE CraniofacialAtlas 11.9 +27.6 27576 1.2 CEBPA CEBPB EZH2 YY1 CEBPG POLR2A RCOR1 HNF4A NFIL3 RXRA SRRM4 piR-49645-001 piR-38351-119 HSPB8
GH12J119087 Enhancer 0.7 Ensembl ENCODE 11.8 +108.0 107967 3.4 CREB1 POLR2A YY1 ETS1 ZNF513 NANOG SP1 POU5F1 ENSG00000257095 SRRM4 piR-32769-003 piR-57965-015 HSPB8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SRRM4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SRRM4

Genomic Locations for SRRM4 Gene

Genomic Locations for SRRM4 Gene
chr12:118,981,541-119,163,051
(GRCh38/hg38)
Size:
181,511 bases
Orientation:
Plus strand
chr12:119,419,300-119,600,856
(GRCh37/hg19)
Size:
181,557 bases
Orientation:
Plus strand

Genomic View for SRRM4 Gene

Genes around SRRM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SRRM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SRRM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SRRM4 Gene

Proteins for SRRM4 Gene

  • Protein details for SRRM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A7MD48-SRRM4_HUMAN
    Recommended name:
    Serine/arginine repetitive matrix protein 4
    Protein Accession:
    A7MD48
    Secondary Accessions:
    • A8K5P6
    • B2RZH7
    • Q7Z5F0
    • Q96JH4

    Protein attributes for SRRM4 Gene

    Size:
    611 amino acids
    Molecular mass:
    68559 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB47482.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SRRM4 Gene

Post-translational modifications for SRRM4 Gene

Other Protein References for SRRM4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SRRM4 Gene

Domains & Families for SRRM4 Gene

Gene Families for SRRM4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SRRM4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SRRM4 Gene

GenScript: Design optimal peptide antigens:
  • Neural-specific serine/arginine repetitive splicing factor of 100 kDa (SRRM4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A7MD48

UniProtKB/Swiss-Prot:

SRRM4_HUMAN :
  • Belongs to the nSR100 family.
Family:
  • Belongs to the nSR100 family.
genes like me logo Genes that share domains with SRRM4: view

Function for SRRM4 Gene

Molecular function for SRRM4 Gene

UniProtKB/Swiss-Prot Function:
Splicing factor specifically required for neural cell differentiation. Acts in conjunction 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). Promotes alternative splicing of REST transcripts to produce REST isoform 3 (REST4) with greatly reduced repressive activity, thereby activating expression of REST targets in neural cells (PubMed:30684677). Plays an important role during embryonic development as well as in the proper functioning of the adult nervous system. Regulates alternative splicing events in genes with important neuronal functions (By similarity).

Phenotypes From GWAS Catalog for SRRM4 Gene

Gene Ontology (GO) - Molecular Function for SRRM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0003729 mRNA binding IEA,ISS --
genes like me logo Genes that share ontologies with SRRM4: view
genes like me logo Genes that share phenotypes with SRRM4: view

Animal Models for SRRM4 Gene

MGI Knock Outs for SRRM4:
  • Srrm4 Srrm4<tm1b(EUCOMM)Wtsi>
  • Srrm4 Srrm4<tm1e(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for SRRM4 Gene

miRTarBase miRNAs that target SRRM4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SRRM4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SRRM4 Gene

Localization for SRRM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SRRM4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SRRM4 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SRRM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,ISS --
genes like me logo Genes that share ontologies with SRRM4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SRRM4 Gene

Pathways & Interactions for SRRM4 Gene

PathCards logo

SuperPathways for SRRM4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SRRM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IEA,ISS --
GO:0006397 mRNA processing IBA,ISS --
GO:0007399 nervous system development IEA,ISS --
GO:0007605 sensory perception of sound IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SRRM4: view

No data available for Pathways by source and SIGNOR curated interactions for SRRM4 Gene

Drugs & Compounds for SRRM4 Gene

No Compound Related Data Available

Transcripts for SRRM4 Gene

mRNA/cDNA for SRRM4 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SRRM4

Alternative Splicing Database (ASD) splice patterns (SP) for SRRM4 Gene

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

Relevant External Links for SRRM4 Gene

GeneLoc Exon Structure for
SRRM4

Expression for SRRM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SRRM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SRRM4 Gene

This gene is overexpressed in Brain - Cerebellum (x13.4), Brain - Cerebellar Hemisphere (x12.6), Brain - Cortex (x5.7), Brain - Frontal Cortex (BA9) (x5.2), and Brain - Anterior cingulate cortex (BA24) (x4.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SRRM4 Gene



Protein tissue co-expression partners for SRRM4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SRRM4

SOURCE GeneReport for Unigene cluster for SRRM4 Gene:

Hs.744964

mRNA Expression by UniProt/SwissProt for SRRM4 Gene:

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

Evidence on tissue expression from TISSUES for SRRM4 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with SRRM4: view

No data available for Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SRRM4 Gene

Orthologs for SRRM4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SRRM4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SRRM4 30 31
  • 99.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SRRM4 30 31
  • 90.58 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SRRM4 30 31
  • 89.97 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Srrm4 30 17 31
  • 85.2 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SRRM4 31
  • 57 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SRRM4 31
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 69 (a)
OneToMany
SRRM4 30
  • 66.02 (n)
-- 31
  • 61 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia SRRM4 31
  • 53 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii SRRM4 31
  • 52 (a)
OneToOne
Species where no ortholog for SRRM4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SRRM4 Gene

ENSEMBL:
Gene Tree for SRRM4 (if available)
TreeFam:
Gene Tree for SRRM4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SRRM4: view image

Paralogs for SRRM4 Gene

No data available for Paralogs for SRRM4 Gene

Variants for SRRM4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SRRM4 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs1555219792 Uncertain Significance: not provided 119,120,278(+) T/C SPLICE_DONOR_VARIANT
rs2555273 - p.Arg547Ser
rs2723880 - p.Arg406Gln
rs7297606 - p.Ser243Asn

Additional dbSNP identifiers (rs#s) for SRRM4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SRRM4 Gene

Variant ID Type Subtype PubMed ID
dgv1564n100 CNV loss 25217958
dgv309n67 CNV loss 20364138
esv2659059 CNV deletion 23128226
esv2665881 CNV deletion 23128226
esv2669850 CNV deletion 23128226
esv2746456 CNV deletion 23290073
esv275551 CNV gain+loss 21479260
esv3580498 CNV loss 25503493
esv3630896 CNV loss 21293372
esv3630897 CNV loss 21293372
esv3630898 CNV loss 21293372
esv3630899 CNV loss 21293372
nsv1069698 CNV deletion 25765185
nsv438238 CNV loss 16468122
nsv455725 CNV loss 19166990
nsv521985 CNV loss 19592680
nsv529044 CNV loss 19592680
nsv560395 CNV loss 21841781
nsv902 CNV deletion 18451855

Variation tolerance for SRRM4 Gene

Residual Variation Intolerance Score: 58.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.70; 91.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SRRM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SRRM4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SRRM4 Gene

Disorders for SRRM4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SRRM4 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SRRM4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SRRM4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SRRM4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SRRM4 Gene

Publications for SRRM4 Gene

  1. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. (PMID: 19737518) Calarco JA … Blencowe BJ (Cell 2009) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PMID: 12800201) Behrends U … Mautner J (International journal of cancer 2003) 3 4
  5. 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. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4

Products for SRRM4 Gene

  • Biorbyt antibodies for SRRM4
  • Signalway Proteins for SRRM4

Sources for SRRM4 Gene