Aliases for SRRM1 Gene

Aliases for SRRM1 Gene

  • Serine And Arginine Repetitive Matrix 1 2 3 5
  • Ser/Arg-Related Nuclear Matrix Protein 2 3 4
  • SR-Related Nuclear Matrix Protein Of 160 KDa 3 4
  • Serine/Arginine Repetitive Matrix Protein 1 3 4
  • SRM160 3 4
  • Serine/Arginine Repetitive Matrix 1 2
  • Plenty Of Prolines 101-Like 2
  • 160-KD 3
  • POP101 3
  • SRm160 4

External Ids for SRRM1 Gene

Previous GeneCards Identifiers for SRRM1 Gene

  • GC01P024494
  • GC01P024039
  • GC01P9A0058
  • GC01P9A4320
  • GC01P9A4714
  • GC01P024714
  • GC01P024842
  • GC01P024958
  • GC01P023226

Summaries for SRRM1 Gene

GeneCards Summary for SRRM1 Gene

SRRM1 (Serine And Arginine Repetitive Matrix 1) is a Protein Coding gene. Diseases associated with SRRM1 include Cortical Thymoma and Epithelial Malignant Thymoma. Among its related pathways are Gene Expression and Transport of Mature Transcript to Cytoplasm.

UniProtKB/Swiss-Prot Summary for SRRM1 Gene

  • Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.

Gene Wiki entry for SRRM1 Gene

Additional gene information for SRRM1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SRRM1 Gene

Genomics for SRRM1 Gene

GeneHancer (GH) Regulatory Elements for SRRM1 Gene

Promoters and enhancers for SRRM1 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
GH01J024641 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 534.5 +11.6 11620 4.3 HNRNPK ZNF217 EP300 NRF1 POLR2G USF1 SP1 PHF8 ZFX ZNF639 SRRM1 SRSF10 SYF2 RPL11 PNRC2 ELOA NCMAP ENSG00000261349 FUCA1 RUNX3
GH01J024632 Enhancer 0.5 Ensembl 500.7 +1.1 1085 0.4 ZNF217 CUX1 GATA3 FOXA1 DPF2 EGR2 FOXA2 SRRM1 lnc-SRRM1-1 NCMAP RNU6-1208P piR-50437-022
GH01J023691 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 66.8 -939.1 -939118 3.2 ZBTB40 ZNF217 EP300 CTCF SIN3A NRF1 TCF12 MYC POLR2G SP1 RPL11 SRSF10 SRRM1 HNRNPR LINC01355 PNRC2 KDM1A ELOA ZNF436 lnc-GALE-4
GH01J025030 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 43.4 +401.3 401281 5.1 SIN3A SP1 EP300 ZIC2 RELA MEF2C RCOR1 ZNF662 REST TRIM22 LINC02793 lnc-CLIC4-2 SRRM1 MAN1C1 RUNX3 SYF2 ENSG00000229162 ENSG00000261349 RSRP1
GH01J024411 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 33.5 -216.0 -215957 8.4 ZBTB40 ZNF217 CTCF SIN3A NRF1 POLR2G USF1 SP1 PHF8 PHB2 STPG1 NIPAL3 NONHSAG000695.2 lnc-IFNLR1-3 SRRM1 SRSF10 ELOA RCAN3 SYF2 NCMAP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SRRM1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SRRM1

Top Transcription factor binding sites by QIAGEN in the SRRM1 gene promoter:
  • aMEF-2
  • LUN-1
  • MEF-2
  • MEF-2A
  • MZF-1
  • NF-1
  • Pax-2
  • Pax-2a
  • POU2F1
  • POU2F1a

Genomic Locations for SRRM1 Gene

Genomic Locations for SRRM1 Gene
chr1:24,631,716-24,673,281
(GRCh38/hg38)
Size:
41,566 bases
Orientation:
Plus strand
chr1:24,958,207-24,999,772
(GRCh37/hg19)
Size:
41,566 bases
Orientation:
Plus strand

Genomic View for SRRM1 Gene

Genes around SRRM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SRRM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SRRM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SRRM1 Gene

Proteins for SRRM1 Gene

  • Protein details for SRRM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IYB3-SRRM1_HUMAN
    Recommended name:
    Serine/arginine repetitive matrix protein 1
    Protein Accession:
    Q8IYB3
    Secondary Accessions:
    • O60585
    • Q5VVN4

    Protein attributes for SRRM1 Gene

    Size:
    904 amino acids
    Molecular mass:
    102335 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Found in a pre-mRNA splicing complex with SFRS4, SFRS5, SNRP70, SNRPA1, SRRM1 and SRRM2. Found in a pre-mRNA exonic splicing enhancer (ESE) complex with SNRP70, SNRPA1, SRRM1 and TRA2B/SFRS10. Found in a mRNA splicing-dependent exon junction complex (EJC) with DEK, PRPF8, NCBP1, RBM8A, RNPS1, SRRM1 and ALYREF/THOC4. Interacts with BAT1, CPSF1, RBM8A, RNPS1, and ALYREF/THOC4. Seems to be a compound of RNA export complexes that are released from speckles in a ATP-dependent manner.
    SequenceCaution:
    • Sequence=AAC09321.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAP97290.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SRRM1 Gene

    Alternative splice isoforms for SRRM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SRRM1 Gene

Post-translational modifications for SRRM1 Gene

  • Phosphorylated on multiple serine and threonine residues by DYRK3 during the G2-to-M transition, after the nuclear-envelope breakdown (PubMed:29973724). Phosphorylation by DYRK3 promotes disassembly of nuclear speckles (PubMed:29973724).
  • Citrullinated by PADI4.
  • Ubiquitination at Lys49 and Lys54
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SRRM1 Gene

Domains & Families for SRRM1 Gene

Gene Families for SRRM1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Protein Domains for SRRM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SRRM1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57710, highly similar to Serine/arginine repetitive matrix protein 1 (B4DED5_HUMAN)
  • Ser/Arg-related nuclear matrix protein (SRRM1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IYB3

UniProtKB/Swiss-Prot:

SRRM1_HUMAN :
  • Belongs to the splicing factor SR family.
Family:
  • Belongs to the splicing factor SR family.
genes like me logo Genes that share domains with SRRM1: view

Function for SRRM1 Gene

Molecular function for SRRM1 Gene

UniProtKB/Swiss-Prot Function:
Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.

Phenotypes From GWAS Catalog for SRRM1 Gene

Gene Ontology (GO) - Molecular Function for SRRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA,IEA 22681889
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SRRM1: view
genes like me logo Genes that share phenotypes with SRRM1: view

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for SRRM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SRRM1 Gene

Localization for SRRM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SRRM1 Gene

Nucleus matrix. Nucleus speckle.

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 SRRM1 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SRRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 9531537
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005829 cytosol TAS --
GO:0016363 nuclear matrix IEA --
genes like me logo Genes that share ontologies with SRRM1: view

Pathways & Interactions for SRRM1 Gene

genes like me logo Genes that share pathways with SRRM1: view

Pathways by source for SRRM1 Gene

Gene Ontology (GO) - Biological Process for SRRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 9531537
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with SRRM1: view

No data available for SIGNOR curated interactions for SRRM1 Gene

Drugs & Compounds for SRRM1 Gene

No Compound Related Data Available

Transcripts for SRRM1 Gene

mRNA/cDNA for SRRM1 Gene

35 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
23 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SRRM1

Alternative Splicing Database (ASD) splice patterns (SP) for SRRM1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15a · 15b · 15c ^ 16 ^ 17 ^
SP1: - - -
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: - -
SP12:

ExUns: 18a · 18b ^ 19 ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for SRRM1 Gene

GeneLoc Exon Structure for
SRRM1

Expression for SRRM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SRRM1 Gene

Protein differential expression in normal tissues from HIPED for SRRM1 Gene

This gene is overexpressed in Lavage (17.4), Serum (10.7), and Peripheral blood mononuclear cells (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SRRM1 Gene



Protein tissue co-expression partners for SRRM1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SRRM1

SOURCE GeneReport for Unigene cluster for SRRM1 Gene:

Hs.18192

Evidence on tissue expression from TISSUES for SRRM1 Gene

  • Liver(4.6)
  • Blood(4.5)
  • Nervous system(4.4)
  • Kidney(2.4)
  • Intestine(2.3)
  • Skin(2.2)
  • Lung(2.1)
  • Muscle(2.1)
  • Eye(2)
genes like me logo Genes that share expression patterns with SRRM1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SRRM1 Gene

Orthologs for SRRM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SRRM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SRRM1 31 30
  • 99.85 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SRRM1 31
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 31
  • 97 (a)
OneToMany
SRRM1 30
  • 93.44 (n)
-- 31
  • 89 (a)
OneToMany
-- 31
  • 84 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Srrm1 31
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SRRM1 31
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SRRM1 31
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves SRRM1 31
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SRRM1 31
  • 85 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii srrm1 31
  • 58 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG11274 32
  • 64 (a)
SRm160 31
  • 28 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea rsr-1 31 32
  • 42 (a)
OneToOne
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6562 30
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3168 31
  • 65 (a)
OneToOne
Cin.4860 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4860 30
Species where no ortholog for SRRM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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 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)

Evolution for SRRM1 Gene

ENSEMBL:
Gene Tree for SRRM1 (if available)
TreeFam:
Gene Tree for SRRM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SRRM1: view image

Paralogs for SRRM1 Gene

Pseudogenes.org Pseudogenes for SRRM1 Gene

genes like me logo Genes that share paralogs with SRRM1: view

No data available for Paralogs for SRRM1 Gene

Variants for SRRM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SRRM1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs17857102 - p.Arg170His

Additional dbSNP identifiers (rs#s) for SRRM1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SRRM1 Gene

Variant ID Type Subtype PubMed ID
esv2745519 CNV deletion 23290073
nsv460862 CNV loss 19166990
nsv545824 CNV loss 21841781
nsv834458 CNV loss 17160897
nsv945828 CNV duplication 23825009
nsv947416 CNV duplication 23825009

Variation tolerance for SRRM1 Gene

Residual Variation Intolerance Score: 19.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.05; 37.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SRRM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SRRM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SRRM1 Gene

Disorders for SRRM1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SRRM1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cortical thymoma
  • polygonal cell thymoma
epithelial malignant thymoma
  • squamoid thymoma
dendritic cell thymoma
  • epithelioid thymoma
- elite association - COSMIC cancer census association via MalaCards
Search SRRM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SRRM1

genes like me logo Genes that share disorders with SRRM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SRRM1 Gene

Publications for SRRM1 Gene

  1. A coactivator of pre-mRNA splicing. (PMID: 9531537) Blencowe BJ … Sharp PA (Genes & development 1998) 2 3 4 23 54
  2. The spatial targeting and nuclear matrix binding domains of SRm160. (PMID: 12624182) Wagner S … Nickerson JA (Proceedings of the National Academy of Sciences of the United States of America 2003) 3 4 23 54
  3. The SRm160/300 splicing coactivator is required for exon-enhancer function. (PMID: 10339552) Eldridge AG … Blencowe BJ (Proceedings of the National Academy of Sciences of the United States of America 1999) 3 4 23 54
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  5. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4 54

Products for SRRM1 Gene

Sources for SRRM1 Gene