Human Gene SND1 (uc003vmi.3)
  Description: Homo sapiens staphylococcal nuclease and tudor domain containing 1 (SND1), mRNA.
RefSeq Summary (NM_014390): This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr7:127,292,202-127,732,659 Size: 440,458 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr7:127,292,428-127,732,110 Size: 439,683 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:127,292,202-127,732,659)mRNA (may differ from genome)Protein (910 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer
GeneCardsGeneNetworkH-INVHGNCHPRDLynx
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SND1_HUMAN
DESCRIPTION: RecName: Full=Staphylococcal nuclease domain-containing protein 1; AltName: Full=100 kDa coactivator; AltName: Full=EBNA2 coactivator p100; AltName: Full=Tudor domain-containing protein 11; AltName: Full=p100 co-activator;
FUNCTION: Functions as a bridging factor between STAT6 and the basal transcription factor. Plays a role in PIM1 regulation of MYB activity. Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2).
SUBUNIT: Binds to acidic transactivation domain of EBNA2. Interacts with EAV NSP1. Interacts with GTF2E1 and GTF2E2. Forms a ternary complex with STAT6 and POLR2A. Interacts with STAT5 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Melanosome. Note=In IL-4 stimulated cells colocalizes with STAT6 in the nucleus. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Phosphorylated by PIM1 in vitro.
SIMILARITY: Contains 4 TNase-like domains.
SIMILARITY: Contains 1 Tudor domain.
SEQUENCE CAUTION: Sequence=AAA80488.1; Type=Frameshift; Positions=5; Note=The frameshift leads to wrong initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SND1
CDC HuGE Published Literature: SND1
Positive Disease Associations: Cholesterol, LDL , Mental Competency
Related Studies:
  1. Cholesterol, LDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Mental Competency
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.

-  MalaCards Disease Associations
  MalaCards Gene Search: SND1
Diseases sorted by gene-association score: myasthenic syndrome, congenital, 7, presynaptic (11), pituitary-dependent cushing's disease (5)

-  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: 70.05 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1260.39 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 -75.10226-0.332 Picture PostScript Text
3' UTR -199.41549-0.363 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
IPR016685 - Silence_cplx_Nase-comp_TudorSN
IPR016071 - Staphylococal_nuclease_OB-fold
IPR006021 - Staphylococcal_nuclease
IPR002071 - Thermonucl_AS
IPR002999 - Tudor

Pfam Domains:
PF00565 - Staphylococcal nuclease homologue
PF00567 - Tudor domain

SCOP Domains:
63748 - Tudor/PWWP/MBT
50199 - Staphylococcal nuclease

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2E6N - NMR MuPIT 2HQE - X-ray MuPIT 2HQX - X-ray MuPIT 2O4X - X-ray MuPIT 3BDL - X-ray MuPIT 3OMC - X-ray MuPIT 3OMG - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q7KZF4
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003712 transcription cofactor activity
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0005515 protein binding
GO:0045296 cadherin binding

Biological Process:
GO:0001649 osteoblast differentiation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006401 RNA catabolic process
GO:0016032 viral process
GO:0031047 gene silencing by RNA
GO:0090305 nucleic acid phosphodiester bond hydrolysis

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016442 RISC complex
GO:0042470 melanosome
GO:0070062 extracellular exosome
GO:0097433 dense body


-  Descriptions from all associated GenBank mRNAs
  LF207053 - JP 2014500723-A/14556: Polycomb-Associated Non-Coding RNAs.
JX013981 - Homo sapiens SND1-BRAF fusion mRNA, complete cds.
U22055 - Human 100 kDa coactivator mRNA, complete cds.
BC017180 - Homo sapiens staphylococcal nuclease and tudor domain containing 1, mRNA (cDNA clone MGC:790 IMAGE:3345037), complete cds.
AK304181 - Homo sapiens cDNA FLJ54574 complete cds, highly similar to Staphylococcal nuclease domain-containing protein 1.
AK096583 - Homo sapiens cDNA FLJ39264 fis, clone OCBBF2009603, highly similar to Staphylococcal nuclease domain-containing protein 1.
AK312313 - Homo sapiens cDNA, FLJ92620, highly similar to Homo sapiens staphylococcal nuclease domain containing 1 (SND1),mRNA.
AB209510 - Homo sapiens mRNA for EBNA-2 co-activator variant protein.
HM005589 - Homo sapiens clone HTL-S-49 testis tissue sperm-binding protein Li 82P mRNA, complete cds.
AB384959 - Synthetic construct DNA, clone: pF1KB4563, Homo sapiens SND1 gene for staphylococcal nuclease domain-containing protein 1, complete cds, without stop codon, in Flexi system.
DQ895529 - Synthetic construct Homo sapiens clone IMAGE:100009989; FLH185283.01L; RZPDo839H05145D staphylococcal nuclease domain containing 1 (SND1) gene, encodes complete protein.
DQ893632 - Synthetic construct clone IMAGE:100006262; FLH185287.01X; RZPDo839H05146D staphylococcal nuclease domain containing 1 (SND1) gene, encodes complete protein.
BT009785 - Homo sapiens EBNA-2 co-activator (100kD) mRNA, complete cds.
AK309014 - Homo sapiens cDNA, FLJ99055.
MA442630 - JP 2018138019-A/14556: Polycomb-Associated Non-Coding RNAs.
AY273894 - Homo sapiens 100 kDa coactivator mRNA, partial cds.
JD416914 - Sequence 397938 from Patent EP1572962.
LF360613 - JP 2014500723-A/168116: Polycomb-Associated Non-Coding RNAs.
LF360618 - JP 2014500723-A/168121: Polycomb-Associated Non-Coding RNAs.
LF360619 - JP 2014500723-A/168122: Polycomb-Associated Non-Coding RNAs.
LF360624 - JP 2014500723-A/168127: Polycomb-Associated Non-Coding RNAs.
LF360625 - JP 2014500723-A/168128: Polycomb-Associated Non-Coding RNAs.
DQ587017 - Homo sapiens piRNA piR-54129, complete sequence.
LF360626 - JP 2014500723-A/168129: Polycomb-Associated Non-Coding RNAs.
LF360633 - JP 2014500723-A/168136: Polycomb-Associated Non-Coding RNAs.
MA596190 - JP 2018138019-A/168116: Polycomb-Associated Non-Coding RNAs.
MA596195 - JP 2018138019-A/168121: Polycomb-Associated Non-Coding RNAs.
MA596196 - JP 2018138019-A/168122: Polycomb-Associated Non-Coding RNAs.
MA596201 - JP 2018138019-A/168127: Polycomb-Associated Non-Coding RNAs.
MA596202 - JP 2018138019-A/168128: Polycomb-Associated Non-Coding RNAs.
MA596203 - JP 2018138019-A/168129: Polycomb-Associated Non-Coding RNAs.
MA596210 - JP 2018138019-A/168136: Polycomb-Associated Non-Coding RNAs.
LF360709 - JP 2014500723-A/168212: Polycomb-Associated Non-Coding RNAs.
LF360731 - JP 2014500723-A/168234: Polycomb-Associated Non-Coding RNAs.
MA596286 - JP 2018138019-A/168212: Polycomb-Associated Non-Coding RNAs.
MA596308 - JP 2018138019-A/168234: Polycomb-Associated Non-Coding RNAs.
LF360823 - JP 2014500723-A/168326: Polycomb-Associated Non-Coding RNAs.
LF360829 - JP 2014500723-A/168332: Polycomb-Associated Non-Coding RNAs.
BC020423 - Homo sapiens staphylococcal nuclease and tudor domain containing 1, mRNA (cDNA clone IMAGE:4177598).
LF360831 - JP 2014500723-A/168334: Polycomb-Associated Non-Coding RNAs.
JD315674 - Sequence 296698 from Patent EP1572962.
JD226703 - Sequence 207727 from Patent EP1572962.
JD261342 - Sequence 242366 from Patent EP1572962.
JD233836 - Sequence 214860 from Patent EP1572962.
JD257215 - Sequence 238239 from Patent EP1572962.
JD195948 - Sequence 176972 from Patent EP1572962.
JD245837 - Sequence 226861 from Patent EP1572962.
LF360832 - JP 2014500723-A/168335: Polycomb-Associated Non-Coding RNAs.
JD410431 - Sequence 391455 from Patent EP1572962.
JD549192 - Sequence 530216 from Patent EP1572962.
JD549641 - Sequence 530665 from Patent EP1572962.
MA596400 - JP 2018138019-A/168326: Polycomb-Associated Non-Coding RNAs.
MA596406 - JP 2018138019-A/168332: Polycomb-Associated Non-Coding RNAs.
MA596408 - JP 2018138019-A/168334: Polycomb-Associated Non-Coding RNAs.
MA596409 - JP 2018138019-A/168335: Polycomb-Associated Non-Coding RNAs.

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

Protein Q7KZF4 (Reactome details) participates in the following event(s):

R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_014390, NP_055205, Q13122, Q7KZF4, Q96AG0, SND1_HUMAN, TDRD11
UCSC ID: uc003vmi.3
RefSeq Accession: NM_014390
Protein: Q7KZF4 (aka SND1_HUMAN)
CCDS: CCDS34747.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014390.2
exon count: 24CDS single in 3' UTR: no RNA size: 3522
ORF size: 2733CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5666.00frame shift in genome: no % Coverage: 99.60
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.