Human Gene SRRM1 (ENST00000323848.14_10) from GENCODE V47lift37
  Description: serine and arginine repetitive matrix 1, transcript variant 40 (from RefSeq NR_159389.1)
Gencode Transcript: ENST00000323848.14_10
Gencode Gene: ENSG00000133226.19_16
Transcript (Including UTRs)
   Position: hg19 chr1:24,969,793-24,999,772 Size: 29,980 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr1:24,969,818-24,998,777 Size: 28,960 Coding Exon Count: 17 

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 (chr1:24,969,793-24,999,772)mRNA (may differ from genome)Protein (904 aa)
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-  Comments and Description Text from UniProtKB
  ID: SRRM1_HUMAN
DESCRIPTION: RecName: Full=Serine/arginine repetitive matrix protein 1; AltName: Full=SR-related nuclear matrix protein of 160 kDa; Short=SRm160; AltName: Full=Ser/Arg-related nuclear matrix protein;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Nucleus matrix. Nucleus speckle.
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 1 PWI domain.
SEQUENCE CAUTION: Sequence=AAC09321.1; Type=Frameshift; Positions=791; Sequence=AAP97290.1; Type=Frameshift; Positions=791;

-  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: 53.24 RPKM in Ovary
Total median expression: 1266.39 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 -5.5025-0.220 Picture PostScript Text
3' UTR -220.10995-0.221 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
IPR002483 - PWI

Pfam Domains:
PF01480 - PWI domain

SCOP Domains:
101233 - PWI domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1MP1 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q8IYB3
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  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0008380 RNA splicing
GO:0031124 mRNA 3'-end processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0016363 nuclear matrix
GO:0016607 nuclear speck
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AF419855 - Homo sapiens Ser/Arg-related nuclear matrix protein (SRRM1) mRNA, complete cds.
BC011019 - Homo sapiens serine/arginine repetitive matrix 1, mRNA (cDNA clone IMAGE:4287134), with apparent retained intron.
BC036187 - Homo sapiens serine/arginine repetitive matrix 1, mRNA (cDNA clone MGC:39488 IMAGE:4827738), complete cds.
AK302498 - Homo sapiens cDNA FLJ61739 complete cds, highly similar to Serine/arginine repetitive matrix protein 1.
BC017315 - Homo sapiens serine/arginine repetitive matrix 1, mRNA (cDNA clone IMAGE:3937531), partial cds.
AF048977 - Homo sapiens Ser/Arg-related nuclear matrix protein (SRM160) mRNA, complete cds.
KU178512 - Homo sapiens serine/arginine repetitive matrix 1 isoform 1 (SRRM1) mRNA, partial cds.
KU178513 - Homo sapiens serine/arginine repetitive matrix 1 isoform 2 (SRRM1) mRNA, partial cds, alternatively spliced.
AK307419 - Homo sapiens cDNA, FLJ97367.
AK307568 - Homo sapiens cDNA, FLJ97516.
AK293576 - Homo sapiens cDNA FLJ57710 complete cds, highly similar to Serine/arginine repetitive matrix protein 1.
JD341942 - Sequence 322966 from Patent EP1572962.
JD311113 - Sequence 292137 from Patent EP1572962.
JD427456 - Sequence 408480 from Patent EP1572962.
JD571856 - Sequence 3 from Patent WO2015030616.
JD371895 - Sequence 352919 from Patent EP1572962.
JD264373 - Sequence 245397 from Patent EP1572962.
JD092124 - Sequence 73148 from Patent EP1572962.
JD336454 - Sequence 317478 from Patent EP1572962.
JD461377 - Sequence 442401 from Patent EP1572962.
JD538445 - Sequence 519469 from Patent EP1572962.
JD170371 - Sequence 151395 from Patent EP1572962.
JD415707 - Sequence 396731 from Patent EP1572962.
JD496771 - Sequence 477795 from Patent EP1572962.
JD183144 - Sequence 164168 from Patent EP1572962.
JD315510 - Sequence 296534 from Patent EP1572962.

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

Protein Q8IYB3 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72124 Formation of the Spliceosomal A 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-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72187 mRNA 3'-end processing
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000323848.1, ENST00000323848.10, ENST00000323848.11, ENST00000323848.12, ENST00000323848.13, ENST00000323848.2, ENST00000323848.3, ENST00000323848.4, ENST00000323848.5, ENST00000323848.6, ENST00000323848.7, ENST00000323848.8, ENST00000323848.9, NR_159389, O60585, Q5VVN4, Q8IYB3, SRM160, SRRM1_HUMAN, uc317rnu.1, uc317rnu.2
UCSC ID: ENST00000323848.14_10
RefSeq Accession: NM_005839.4
Protein: Q8IYB3 (aka SRRM1_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.