SpermatogenesisOnline 1.0

Tag Content
SG ID
SG00013353 
UniProt Accession
Theoretical PI
5.87  
Molecular Weight
94630 Da  
Genbank Nucleotide ID
Genbank Protein ID
Gene Name
Matr3 
Gene Synonyms/Alias
 
Protein Name
Matrin-3 
Protein Synonyms/Alias
 
Organism
Mus musculus (Mouse) 
NCBI Taxonomy ID
10090 
Chromosome Location
chr:18;35721812-35751699;1
View in Ensembl genome browser  
Function in Stage
Uncertain 
Function in Cell Type
Uncertain 
Probability (GAS) of Function in Spermatogenesis
0.648608552 
The probability was calculated by GAS algorithm, ranging from 0 to 1. The closer it is to 1, the more possibly it functions in spermatogenesis.
Description
Temporarily unavailable 
Abstract of related literatures
1. This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. PMID: [16141072] 

2. The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline. PMID: [15489334] 

3. In the mammalian central nervous system, the structure known as the postsynaptic density (PSD) is a dense complex of proteins whose function is to detect and respond to neurotransmitter released from presynaptic axon terminals. Regulation of protein phosphorylation in this molecular machinery is critical to the activity of its components, which include neurotransmitter receptors, kinases/phosphatases, scaffolding molecules, and proteins regulating cytoskeletal structure. To characterize the phosphorylation state of proteins in PSD samples, we combined strong cation exchange (SCX) chromatography with IMAC. Initially, tryptic peptides were separated by cation exchange and analyzed by reverse phase chromatography coupled to tandem mass spectrometry, which led to the identification of phosphopeptides in most SCX fractions. Because each of these individual fractions was too complex to characterize completely in single LC-MS/MS runs, we enriched for phosphopeptides by performing IMAC on each SCX fraction, yielding at least a 3-fold increase in identified phosphopeptides relative to either approach alone (SCX or IMAC). This enabled us to identify at least one site of phosphorylation on 23% (287 of 1,264) of all proteins found to be present in the postsynaptic density preparation. In total, we identified 998 unique phosphorylated peptides, mapping to 723 unique sites of phosphorylation. At least one exact site of phosphorylation was determined on 62% (621 of 998) of all phosphopeptides, and approximately 80% of identified phosphorylation sites are novel. PMID: [16452087] 

4. Protein phosphorylation is a complex network of signaling and regulatory events that affects virtually every cellular process. Our understanding of the nature of this network as a whole remains limited, largely because of an array of technical challenges in the isolation and high-throughput sequencing of phosphorylated species. In the present work, we demonstrate that a combination of tandem phosphopeptide enrichment methods, high performance MS, and optimized database search/data filtering strategies is a powerful tool for surveying the phosphoproteome. Using our integrated analytical platform, we report the identification of 5,635 nonredundant phosphorylation sites from 2,328 proteins from mouse liver. From this list of sites, we extracted both novel and known motifs for specific Ser/Thr kinases including a "dipolar" motif. We also found that C-terminal phosphorylation was more frequent than at any other location and that the distribution of potential kinases for these sites was unique. Finally, we identified double phosphorylation motifs that may be involved in ordered phosphorylation. PMID: [17242355] 

5. Kinases play a prominent role in tumor development, pointing to the presence of specific phosphorylation patterns in tumor tissues. Here, we investigate whether recently developed high resolution mass spectrometric (MS) methods for proteome and phosphoproteome analysis can also be applied to solid tumors. As tumor model, we used TG3 mutant mice carrying skin melanomas. At total of 100 microg of solid tumor lysate yielded a melanoma proteome of 4443 identified proteins, including at least 88 putative melanoma markers previously found by cDNA microarray technology. Analysis of 2 mg of lysate from dissected melanoma with titansphere chromatography and 8 mg with strong cation exchange together resulted in the identification of more than 5600 phosphorylation sites on 2250 proteins. The phosphoproteome included many hits from pathways important in melanoma. One-month storage at -80 degrees C did not significantly decrease the number of identified phosphorylation sites. Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies. PMID: [19367708] 

6. The ability of macrophages to clear pathogens and elicit a sustained immune response is regulated by various cytokines, including interferon-gamma (IFN-gamma). To investigate the molecular mechanisms by which IFN-gamma modulates phagosome functions, we profiled the changes in composition, abundance, and phosphorylation of phagosome proteins in resting and activated macrophages by using quantitative proteomics and bioinformatics approaches. We identified 2415 phagosome proteins together with 2975 unique phosphorylation sites with a high level of sensitivity. Using network analyses, we determined that IFN-gamma delays phagosomal acquisition of lysosomal hydrolases and peptidases for the gain of antigen presentation. Furthermore, this gain in antigen presentation is dependent on phagosomal networks of the actin cytoskeleton and vesicle-trafficking proteins, as well as Src kinases and calpain proteases. Major histocompatibility complex class I antigen-presentation assays validated the molecular participation of these networks in the enhanced capacity of IFN-gamma-activated macrophages to crosspresent exogenous antigens to CD8(+) T cells. PMID: [19144319] 

7. We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment. PMID: [19131326] 

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Function
May play a role in transcription or may interact withother nuclear matrix proteins to form the internal fibrogranularnetwork. In association with the SFPQ-NONO heteromer may play arole in nuclear retention of defective RNAs (By similarity). 
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Subcellular Location
Nucleus matrix (By similarity). 
Tissue Specificity
 
Gene Ontology
GO IDGO termEvidence
GO:0016363 C:nuclear matrix IEA:UniProtKB-SubCell.
GO:0000166 F:nucleotide binding IEA:InterPro.
GO:0003723 F:RNA binding IEA:UniProtKB-KW.
GO:0008270 F:zinc ion binding IEA:InterPro.
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Interpro
IPR012677;    Nucleotide-bd_a/b_plait.
IPR000504;    RRM_dom.
IPR015880;    Znf_C2H2-like.
IPR000690;    Znf_C2H2_matrin.
IPR003604;    Znf_U1.
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Pfam
SMART
SM00360;    RRM;    2.
SM00355;    ZnF_C2H2;    1.
SM00451;    ZnF_U1;    2.
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PROSITE
PS50102;    RRM;    2.
PS50171;    ZF_MATRIN;    1.
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PRINTS
Created Date
18-Oct-2012 
Record Type
GAS predicted 
Sequence Annotation
INIT_MET      1      1       Removed (By similarity).
CHAIN         2    846       Matrin-3.
                             /FTId=PRO_0000081623.
DOMAIN      398    473       RRM 1.
DOMAIN      496    571       RRM 2.
ZN_FING     800    831       Matrin-type.
MOTIF       709    717       Nuclear localization signal (Potential).
MOD_RES       2      2       N-acetylserine (By similarity).
MOD_RES       3      3       N6-acetyllysine (By similarity).
MOD_RES      22     22       Phosphoserine (By similarity).
MOD_RES     118    118       Phosphoserine (By similarity).
MOD_RES     188    188       Phosphoserine.
MOD_RES     195    195       Phosphoserine (By similarity).
MOD_RES     206    206       Phosphoserine (By similarity).
MOD_RES     208    208       Phosphoserine (By similarity).
MOD_RES     397    397       Phosphoserine (By similarity).
MOD_RES     473    473       N6-acetyllysine (By similarity).
MOD_RES     522    522       N6-acetyllysine (By similarity).
MOD_RES     533    533       Phosphoserine (By similarity).
MOD_RES     571    571       N6-acetyllysine (By similarity).
MOD_RES     596    596       Phosphoserine (By similarity).
MOD_RES     598    598       Phosphoserine.
MOD_RES     604    604       Phosphoserine (By similarity).
MOD_RES     606    606       Phosphoserine (By similarity).
MOD_RES     653    653       Phosphoserine (By similarity).
MOD_RES     670    670       Phosphoserine (By similarity).
MOD_RES     672    672       Phosphoserine (By similarity).
MOD_RES     673    673       Phosphoserine (By similarity).
MOD_RES     695    695       Phosphoserine (By similarity).
MOD_RES     772    772       Phosphotyrosine (By similarity).
MOD_RES     835    835       N6-acetyllysine (By similarity).
STRAND      399    404
STRAND      408    410
HELIX       411    416
TURN        417    419
HELIX       420    422
STRAND      425    430
STRAND      432    435
STRAND      437    443
HELIX       444    456
STRAND      467    471
STRAND      497    502
HELIX       511    514
TURN        515    520
STRAND      524    529
TURN        530    533
STRAND      534    538
HELIX       542    554
STRAND      559    562
STRAND      565    569
STRAND      573    576
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Nucleotide Sequence
Length: 3721 bp   Go to nucleotide: FASTA
Protein Sequence
Length: 846 bp   Go to amino acid: FASTA
The verified Protein-Protein interaction information
UniProt
 Gene Symbol Ref Databases
Cacnb4IntAct 
Pou5f1BioGRID 
Rnf2IntAct 
Other Protein-Protein interaction resources
String database  
View Microarray data
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