Human Gene SFMBT1 (ENST00000394752.8_7) from GENCODE V47lift37
  Description: Scm like with four mbt domains 1 (from RefSeq NM_016329.4)
Gencode Transcript: ENST00000394752.8_7
Gencode Gene: ENSG00000163935.14_10
Transcript (Including UTRs)
   Position: hg19 chr3:52,937,588-53,080,089 Size: 142,502 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr3:52,939,152-53,003,144 Size: 63,993 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:52,937,588-53,080,089)mRNA (may differ from genome)Protein (866 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SMBT1_HUMAN
DESCRIPTION: RecName: Full=Scm-like with four MBT domains protein 1; AltName: Full=Renal ubiquitous protein 1;
TISSUE SPECIFICITY: Expressed in all cell lines and normal tissues tested, including the thymus.
MISCELLANEOUS: Ubiquitous self-antigen.
SIMILARITY: Contains 4 MBT repeats.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SFMBT1
Diseases sorted by gene-association score: hydrocephalus (2)

-  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: 29.02 RPKM in Testis
Total median expression: 146.62 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 -154.50388-0.398 Picture PostScript Text
3' UTR -405.201564-0.259 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
IPR021987 - DUF3588
IPR004092 - Mbt
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF02820 - mbt repeat
PF07647 - SAM domain (Sterile alpha motif)
PF12140 - SLED domain

SCOP Domains:
47769 - SAM/Pointed domain
54160 - Chromo domain-like
63748 - Tudor/PWWP/MBT

ModBase Predicted Comparative 3D Structure on Q9UHJ3
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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 SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0042393 histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007283 spermatogenesis
GO:0030154 cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048635 negative regulation of muscle organ development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AL080140 - Homo sapiens mRNA; cDNA DKFZp434L243 (from clone DKFZp434L243).
BC014614 - Homo sapiens Scm-like with four mbt domains 1, mRNA (cDNA clone MGC:3342 IMAGE:3029598), complete cds.
AF168132 - Homo sapiens RU1 (RU1) mRNA, complete cds.
AB189472 - Homo sapiens SFMBT mRNA for Scm-related gene product containing four mbt domains, complete cds.
AK313965 - Homo sapiens cDNA, FLJ94612, highly similar to Homo sapiens Scm-like with four mbt domains 1 (SFMBT1), mRNA.
DQ892861 - Synthetic construct clone IMAGE:100005491; FLH190393.01X; RZPDo839H0975D Scm-like with four mbt domains 1 (SFMBT1) gene, encodes complete protein.
DQ896110 - Synthetic construct Homo sapiens clone IMAGE:100010570; FLH190389.01L; RZPDo839H0965D Scm-like with four mbt domains 1 (SFMBT1) gene, encodes complete protein.
AB587473 - Synthetic construct DNA, clone: pF1KB8506, Homo sapiens SFMBT1 gene for Scm-like with four mbt domains 1, without stop codon, in Flexi system.
JD432919 - Sequence 413943 from Patent EP1572962.
JD062968 - Sequence 43992 from Patent EP1572962.
JD073337 - Sequence 54361 from Patent EP1572962.
JD496805 - Sequence 477829 from Patent EP1572962.
JD102851 - Sequence 83875 from Patent EP1572962.
JD167356 - Sequence 148380 from Patent EP1572962.
JD207002 - Sequence 188026 from Patent EP1572962.
JD304087 - Sequence 285111 from Patent EP1572962.
JD354799 - Sequence 335823 from Patent EP1572962.
JD068009 - Sequence 49033 from Patent EP1572962.
JD037957 - Sequence 18981 from Patent EP1572962.
JD460501 - Sequence 441525 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000394752.1, ENST00000394752.2, ENST00000394752.3, ENST00000394752.4, ENST00000394752.5, ENST00000394752.6, ENST00000394752.7, NM_016329, Q402F7, Q96C73, Q9UHJ3, Q9Y4Q9, RU1, SMBT1_HUMAN, uc318wwn.1, uc318wwn.2
UCSC ID: ENST00000394752.8_7
RefSeq Accession: NM_016329.4
Protein: Q9UHJ3 (aka SMBT1_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.