Human Gene SNAI3 (uc002flj.3) Description and Page Index
  Description: Homo sapiens snail family zinc finger 3 (SNAI3), mRNA.
RefSeq Summary (NM_178310): SNAI3 is a member of the SNAIL gene family, named for the Drosophila snail gene, which plays roles in mesodermal formation during embryogenesis (Katoh and Katoh, 2003 [PubMed 12579345]).[supplied by OMIM, Apr 2009]. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.417785.1, SRR1163655.513820.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN01820689, SAMN01820693 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000332281.6/ ENSP00000327968.5 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:88,744,090-88,752,882 Size: 8,793 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr16:88,744,856-88,752,814 Size: 7,959 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,744,090-88,752,882)mRNA (may differ from genome)Protein (292 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SNAI3_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein SNAI3; AltName: Full=Protein snail homolog 3; AltName: Full=Zinc finger protein 293;
FUNCTION: Seems to inhibit myoblast differentiation. Transcriptional repressor of E-box-dependent transactivation of downstream myogenic bHLHs genes. Binds preferentially to the canonical E-box sequences 5'-CAGGTG-3' and 5'-CACCTG-3' (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
DOMAIN: Binds E-box via C2H2-type zinc finger domain (By similarity).
SIMILARITY: Belongs to the snail C2H2-type zinc-finger protein family.
SIMILARITY: Contains 5 C2H2-type zinc fingers.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.92 RPKM in Whole Blood
Total median expression: 59.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.2068-0.429 Picture PostScript Text
3' UTR -348.64766-0.455 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
IPR002355 - Cu_oxidase_Cu_BS
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF12874 - Zinc-finger of C2H2 type
PF13894 - C2H2-type zinc finger
PF13912 - C2H2-type zinc finger

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on Q3KNW1
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 Details     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000982 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005507 copper ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  BC041461 - Homo sapiens, Similar to snail homolog 3 (Drosophila), clone IMAGE:5209145, mRNA, partial cds.
BC107058 - Homo sapiens snail homolog 3 (Drosophila), mRNA (cDNA clone MGC:129606 IMAGE:40005947), complete cds.
JD184482 - Sequence 165506 from Patent EP1572962.
JD058287 - Sequence 39311 from Patent EP1572962.
JD097147 - Sequence 78171 from Patent EP1572962.
JD188109 - Sequence 169133 from Patent EP1572962.
JD244179 - Sequence 225203 from Patent EP1572962.
JD147128 - Sequence 128152 from Patent EP1572962.
JD101019 - Sequence 82043 from Patent EP1572962.
JD441873 - Sequence 422897 from Patent EP1572962.
JD159439 - Sequence 140463 from Patent EP1572962.
JD399537 - Sequence 380561 from Patent EP1572962.
KJ896031 - Synthetic construct Homo sapiens clone ccsbBroadEn_05425 SNAI3 gene, encodes complete protein.
AB464228 - Synthetic construct DNA, clone: pF1KB7601, Homo sapiens SNAI3 gene for snail homolog 3, without stop codon, in Flexi system.
JD203257 - Sequence 184281 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_178310, NP_840101, Q3KNW1, Q86SU5, SNAI3_HUMAN, ZNF293
UCSC ID: uc002flj.3
RefSeq Accession: NM_178310
Protein: Q3KNW1 (aka SNAI3_HUMAN)
CCDS: CCDS32505.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178310.3
exon count: 3CDS single in 3' UTR: no RNA size: 1713
ORF size: 879CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1958.00frame shift in genome: no % Coverage: 100.00
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.