RGD Reference Report - Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. - Rat Genome Database

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Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

Authors: Chen, YI  Moore, RE  Ge, HY  Young, MK  Lee, TD  Stevens, SW 
Citation: Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
RGD ID: 9686091
Pubmed: PMID:17537823   (View Abstract at PubMed)
PMCID: PMC1919476   (View Article at PubMed Central)
DOI: DOI:10.1093/nar/gkm347   (Journal Full-text)

Previous compositional studies of pre-mRNA processing complexes have been performed in vitro on synthetic pre-mRNAs containing a single intron. To provide a more comprehensive list of polypeptides associated with the pre-mRNA splicing apparatus, we have determined the composition of the bulk pre-mRNA processing machinery in living cells. We purified endogenous nuclear pre-mRNA processing complexes from human and chicken cells comprising the massive (>200S) supraspliceosomes (a.k.a. polyspliceosomes). As expected, RNA components include a heterogeneous mixture of pre-mRNAs and the five spliceosomal snRNAs. In addition to known pre-mRNA splicing factors, 5' end binding factors, 3' end processing factors, mRNA export factors, hnRNPs and other RNA binding proteins, the protein components identified by mass spectrometry include RNA adenosine deaminases and several novel factors. Intriguingly, our purified supraspliceosomes also contain a number of structural proteins, nucleoporins, chromatin remodeling factors and several novel proteins that were absent from splicing complexes assembled in vitro. These in vivo analyses bring the total number of factors associated with pre-mRNA to well over 300, and represent the most comprehensive analysis of the pre-mRNA processing machinery to date.

Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations

TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
spliceosome pathway   TAS 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091; 9686091 RGD 
spliceosome pathway   ISODDX42 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPA0 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPA1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPA2B1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPA3 (Homo sapiens)9686091 RGD 
spliceosome pathway   ISOHNRNPAB (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPC (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPD (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPH1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPH3 (Homo sapiens)9686091 RGD 
spliceosome pathway   ISOHNRNPK (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPL (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPM (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPR (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOHNRNPU (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOLSM2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOLSM3 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOLSM4 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOLSM5 (Homo sapiens)9686091 RGD 
spliceosome pathway   ISOLSM6 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOLSM7 (Homo sapiens)9686091 RGD 
spliceosome pathway   ISOLSM8 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISORBMX (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3A1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3A2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3A3 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B3 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B4 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B5 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSF3B6 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPA1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPB (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPB2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPD1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPD2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPD3 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPE (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPF (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSNRPG (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRRM1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRRM2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF1 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF10 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF11 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF12 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF2 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF3 (Homo sapiens)9686091 RGD 
spliceosome pathway   ISOSRSF4 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF5 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF6 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF7 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSRSF9 (Homo sapiens)9686091; 9686091 RGD 
spliceosome pathway   ISOSYNCRIP (Homo sapiens)9686091; 9686091 RGD 
Objects Annotated

Genes (Rattus norvegicus)
Ddx42  (DEAD-box helicase 42)
Hnrnpa0  (heterogeneous nuclear ribonucleoprotein A0)
Hnrnpa1  (heterogeneous nuclear ribonucleoprotein A1)
Hnrnpa2b1  (heterogeneous nuclear ribonucleoprotein A2/B1)
Hnrnpab  (heterogeneous nuclear ribonucleoprotein A/B)
Hnrnpc  (heterogeneous nuclear ribonucleoprotein C)
Hnrnpd  (heterogeneous nuclear ribonucleoprotein D)
Hnrnph1  (heterogeneous nuclear ribonucleoprotein H1)
Hnrnpk  (heterogeneous nuclear ribonucleoprotein K)
Hnrnpl  (heterogeneous nuclear ribonucleoprotein L)
Hnrnpm  (heterogeneous nuclear ribonucleoprotein M)
Hnrnpr  (heterogeneous nuclear ribonucleoprotein R)
Hnrnpu  (heterogeneous nuclear ribonucleoprotein U)
Lsm2  (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm3  (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm4  (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm6  (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm7  (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm8  (LSM8 homolog, U6 small nuclear RNA associated)
Rbmx  (RNA binding motif protein, X-linked)
Sf3a1  (splicing factor 3A subunit 1)
Sf3a2  (splicing factor 3A subunit 2)
Sf3a3  (splicing factor 3a, subunit 3)
Sf3b1  (splicing factor 3b, subunit 1)
Sf3b2  (splicing factor 3b, subunit 2)
Sf3b3  (splicing factor 3b, subunit 3)
Sf3b4  (splicing factor 3B subunit 4)
Sf3b5  (splicing factor 3b, subunit 5)
Sf3b6  (splicing factor 3B, subunit 6)
Snrpa1  (small nuclear ribonucleoprotein polypeptide A')
Snrpb  (small nuclear ribonucleoprotein polypeptides B and B1)
Snrpb2  (small nuclear ribonucleoprotein polypeptide B2)
Snrpd1  (small nuclear ribonucleoprotein D1 polypeptide)
Snrpd2  (small nuclear ribonucleoprotein D2 polypeptide)
Snrpd3  (small nuclear ribonucleoprotein D3 polypeptide)
Snrpe  (small nuclear ribonucleoprotein polypeptide E)
Snrpf  (small nuclear ribonucleoprotein polypeptide F)
Snrpg  (small nuclear ribonucleoprotein polypeptide G)
Srrm1  (serine and arginine repetitive matrix 1)
Srrm2  (serine/arginine repetitive matrix 2)
Srsf1  (serine and arginine rich splicing factor 1)
Srsf10  (serine and arginine rich splicing factor 10)
Srsf11  (serine and arginine rich splicing factor 11)
Srsf12  (serine and arginine rich splicing factor 12)
Srsf2  (serine and arginine rich splicing factor 2)
Srsf4  (serine and arginine rich splicing factor 4)
Srsf5  (serine and arginine rich splicing factor 5)
Srsf6  (serine and arginine rich splicing factor 6)
Srsf7  (serine and arginine rich splicing factor 7)
Srsf9  (serine and arginine rich splicing factor 9)
Syncrip  (synaptotagmin binding, cytoplasmic RNA interacting protein)

Genes (Mus musculus)
Ddx42  (DEAD box helicase 42)
Hnrnpa0  (heterogeneous nuclear ribonucleoprotein A0)
Hnrnpa1  (heterogeneous nuclear ribonucleoprotein A1)
Hnrnpa2b1  (heterogeneous nuclear ribonucleoprotein A2/B1)
Hnrnpa3  (heterogeneous nuclear ribonucleoprotein A3)
Hnrnpab  (heterogeneous nuclear ribonucleoprotein A/B)
Hnrnpc  (heterogeneous nuclear ribonucleoprotein C)
Hnrnpd  (heterogeneous nuclear ribonucleoprotein D)
Hnrnph1  (heterogeneous nuclear ribonucleoprotein H1)
Hnrnph3  (heterogeneous nuclear ribonucleoprotein H3)
Hnrnpk  (heterogeneous nuclear ribonucleoprotein K)
Hnrnpl  (heterogeneous nuclear ribonucleoprotein L)
Hnrnpm  (heterogeneous nuclear ribonucleoprotein M)
Hnrnpr  (heterogeneous nuclear ribonucleoprotein R)
Hnrnpu  (heterogeneous nuclear ribonucleoprotein U)
Lsm2  (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm3  (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm4  (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm5  (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm6  (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated)
Lsm8  (LSM8 homolog, U6 small nuclear RNA associated)
Rbmx  (RNA binding motif protein, X chromosome)
Sf3a1  (splicing factor 3a, subunit 1)
Sf3a2  (splicing factor 3a, subunit 2)
Sf3a3  (splicing factor 3a, subunit 3)
Sf3b1  (splicing factor 3b, subunit 1)
Sf3b2  (splicing factor 3b, subunit 2)
Sf3b3  (splicing factor 3b, subunit 3)
Sf3b4  (splicing factor 3b, subunit 4)
Sf3b5  (splicing factor 3b, subunit 5)
Sf3b6  (splicing factor 3B, subunit 6)
Snrpa1  (small nuclear ribonucleoprotein polypeptide A')
Snrpb  (small nuclear ribonucleoprotein B)
Snrpb2  (U2 small nuclear ribonucleoprotein B)
Snrpd1  (small nuclear ribonucleoprotein D1)
Snrpd2  (small nuclear ribonucleoprotein D2)
Snrpd3  (small nuclear ribonucleoprotein D3)
Snrpe  (small nuclear ribonucleoprotein E)
Snrpf  (small nuclear ribonucleoprotein polypeptide F)
Snrpg  (small nuclear ribonucleoprotein polypeptide G)
Srrm1  (serine/arginine repetitive matrix 1)
Srrm2  (serine/arginine repetitive matrix 2)
Srsf1  (serine and arginine-rich splicing factor 1)
Srsf10  (serine and arginine-rich splicing factor 10)
Srsf11  (serine and arginine-rich splicing factor 11)
Srsf12  (serine and arginine-rich splicing factor 12)
Srsf2  (serine and arginine-rich splicing factor 2)
Srsf3  (serine and arginine-rich splicing factor 3)
Srsf4  (serine and arginine-rich splicing factor 4)
Srsf5  (serine and arginine-rich splicing factor 5)
Srsf6  (serine and arginine-rich splicing factor 6)
Srsf7  (serine and arginine-rich splicing factor 7)
Srsf9  (serine and arginine-rich splicing factor 9)
Syncrip  (synaptotagmin binding, cytoplasmic RNA interacting protein)

Genes (Homo sapiens)
DDX42  (DEAD-box helicase 42)
HNRNPA0  (heterogeneous nuclear ribonucleoprotein A0)
HNRNPA1  (heterogeneous nuclear ribonucleoprotein A1)
HNRNPA2B1  (heterogeneous nuclear ribonucleoprotein A2/B1)
HNRNPA3  (heterogeneous nuclear ribonucleoprotein A3)
HNRNPAB  (heterogeneous nuclear ribonucleoprotein A/B)
HNRNPC  (heterogeneous nuclear ribonucleoprotein C)
HNRNPD  (heterogeneous nuclear ribonucleoprotein D)
HNRNPH1  (heterogeneous nuclear ribonucleoprotein H1)
HNRNPH3  (heterogeneous nuclear ribonucleoprotein H3)
HNRNPK  (heterogeneous nuclear ribonucleoprotein K)
HNRNPL  (heterogeneous nuclear ribonucleoprotein L)
HNRNPM  (heterogeneous nuclear ribonucleoprotein M)
HNRNPR  (heterogeneous nuclear ribonucleoprotein R)
HNRNPU  (heterogeneous nuclear ribonucleoprotein U)
LSM2  (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM3  (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM4  (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM5  (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM6  (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM7  (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated)
LSM8  (LSM8 homolog, U6 small nuclear RNA associated)
RBMX  (RNA binding motif protein X-linked)
SF3A1  (splicing factor 3a subunit 1)
SF3A2  (splicing factor 3a subunit 2)
SF3A3  (splicing factor 3a subunit 3)
SF3B1  (splicing factor 3b subunit 1)
SF3B2  (splicing factor 3b subunit 2)
SF3B3  (splicing factor 3b subunit 3)
SF3B4  (splicing factor 3b subunit 4)
SF3B5  (splicing factor 3b subunit 5)
SF3B6  (splicing factor 3b subunit 6)
SNRPA1  (small nuclear ribonucleoprotein polypeptide A')
SNRPB  (small nuclear ribonucleoprotein polypeptides B and B1)
SNRPB2  (small nuclear ribonucleoprotein polypeptide B2)
SNRPD1  (small nuclear ribonucleoprotein D1 polypeptide)
SNRPD2  (small nuclear ribonucleoprotein D2 polypeptide)
SNRPD3  (small nuclear ribonucleoprotein D3 polypeptide)
SNRPE  (small nuclear ribonucleoprotein polypeptide E)
SNRPF  (small nuclear ribonucleoprotein polypeptide F)
SNRPG  (small nuclear ribonucleoprotein polypeptide G)
SRRM1  (serine and arginine repetitive matrix 1)
SRRM2  (serine/arginine repetitive matrix 2)
SRSF1  (serine and arginine rich splicing factor 1)
SRSF10  (serine and arginine rich splicing factor 10)
SRSF11  (serine and arginine rich splicing factor 11)
SRSF12  (serine and arginine rich splicing factor 12)
SRSF2  (serine and arginine rich splicing factor 2)
SRSF3  (serine and arginine rich splicing factor 3)
SRSF4  (serine and arginine rich splicing factor 4)
SRSF5  (serine and arginine rich splicing factor 5)
SRSF6  (serine and arginine rich splicing factor 6)
SRSF7  (serine and arginine rich splicing factor 7)
SRSF9  (serine and arginine rich splicing factor 9)
SYNCRIP  (synaptotagmin binding cytoplasmic RNA interacting protein)


Additional Information