Human Gene SAMD4B (ENST00000610417.5_5) from GENCODE V47lift37
  Description: sterile alpha motif domain containing 4B, transcript variant 33 (from RefSeq NR_169273.1)
Gencode Transcript: ENST00000610417.5_5
Gencode Gene: ENSG00000179134.16_10
Transcript (Including UTRs)
   Position: hg19 chr19:39,833,061-39,876,340 Size: 43,280 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr19:39,847,534-39,874,167 Size: 26,634 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:39,833,061-39,876,340)mRNA (may differ from genome)Protein (694 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
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-  Comments and Description Text from UniProtKB
  ID: SMAG2_HUMAN
DESCRIPTION: RecName: Full=Protein Smaug homolog 2; Short=Smaug 2; Short=hSmaug2; AltName: Full=Sterile alpha motif domain-containing protein 4B; Short=SAM domain-containing protein 4B;
FUNCTION: Has transcriptional repressor activity. Overexpression inhibits the transcriptional activities of AP-1, p53/TP53 and CDKN1A.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Widely expressed in embryonic and adult tissues.
SIMILARITY: Belongs to the SMAUG family.
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -209.30422-0.496 Picture PostScript Text
3' UTR -815.202173-0.375 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
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1
IPR015327 - Smaug_PHAT

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF07647 - SAM domain (Sterile alpha motif)

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q5PRF9
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0030371 translation repressor activity

Biological Process:
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0017148 negative regulation of translation
GO:0043488 regulation of mRNA stability

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK001073 - Homo sapiens cDNA FLJ10211 fis, clone HEMBA1006377.
BC054518 - Homo sapiens sterile alpha motif domain containing 4B, mRNA (cDNA clone MGC:60296 IMAGE:6501489), complete cds.
EF601121 - Homo sapiens sterile alpha motif domain containing 4B (SAMD4B) mRNA, complete cds.
BC080641 - Homo sapiens sterile alpha motif domain containing 4B, mRNA (cDNA clone MGC:99832 IMAGE:6645022), complete cds.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
JC506666 - Sequence 34 from Patent EP2733220.
JC737778 - Sequence 34 from Patent WO2014075939.
MP015103 - Sequence 306 from Patent WO2019016252.
JD120669 - Sequence 101693 from Patent EP1572962.
JD226451 - Sequence 207475 from Patent EP1572962.
KJ894127 - Synthetic construct Homo sapiens clone ccsbBroadEn_03521 SAMD4B gene, encodes complete protein.
BC065211 - Homo sapiens sterile alpha motif domain containing 4B, mRNA (cDNA clone IMAGE:3862555), partial cds.
BC039652 - Homo sapiens sterile alpha motif domain containing 4B, mRNA (cDNA clone IMAGE:5018567), partial cds.
JD126439 - Sequence 107463 from Patent EP1572962.
JD070088 - Sequence 51112 from Patent EP1572962.
JD390324 - Sequence 371348 from Patent EP1572962.
AK091041 - Homo sapiens cDNA FLJ33722 fis, clone BRAWH2016800.
JD315946 - Sequence 296970 from Patent EP1572962.
JD410910 - Sequence 391934 from Patent EP1572962.
JD482216 - Sequence 463240 from Patent EP1572962.
JD421643 - Sequence 402667 from Patent EP1572962.
JD077506 - Sequence 58530 from Patent EP1572962.
JD159122 - Sequence 140146 from Patent EP1572962.
JD060088 - Sequence 41112 from Patent EP1572962.
JD537058 - Sequence 518082 from Patent EP1572962.
JD132841 - Sequence 113865 from Patent EP1572962.
JD418632 - Sequence 399656 from Patent EP1572962.
JD487527 - Sequence 468551 from Patent EP1572962.
JD252078 - Sequence 233102 from Patent EP1572962.
JD121749 - Sequence 102773 from Patent EP1572962.
JD439028 - Sequence 420052 from Patent EP1572962.
JD463357 - Sequence 444381 from Patent EP1572962.
JD266335 - Sequence 247359 from Patent EP1572962.
JD471028 - Sequence 452052 from Patent EP1572962.
JD073932 - Sequence 54956 from Patent EP1572962.
JD424428 - Sequence 405452 from Patent EP1572962.
JD363904 - Sequence 344928 from Patent EP1572962.
JD044253 - Sequence 25277 from Patent EP1572962.
JD096017 - Sequence 77041 from Patent EP1572962.
JD108415 - Sequence 89439 from Patent EP1572962.
JD465070 - Sequence 446094 from Patent EP1572962.
JD211998 - Sequence 193022 from Patent EP1572962.
JD411559 - Sequence 392583 from Patent EP1572962.
JD239828 - Sequence 220852 from Patent EP1572962.
JD344169 - Sequence 325193 from Patent EP1572962.
JD323765 - Sequence 304789 from Patent EP1572962.
JD175107 - Sequence 156131 from Patent EP1572962.
JD184271 - Sequence 165295 from Patent EP1572962.
JD491284 - Sequence 472308 from Patent EP1572962.
AK128884 - Homo sapiens cDNA FLJ46916 fis, clone THYMU1000393.

-  Other Names for This Gene
  Alternate Gene Symbols: A5Z0M6, ENST00000610417.1, ENST00000610417.2, ENST00000610417.3, ENST00000610417.4, NR_169273, Q5PRF9, Q6P194, SMAG2_HUMAN, SMAUG2, uc327mtl.1, uc327mtl.2
UCSC ID: ENST00000610417.5_5
RefSeq Accession: NM_001384574.2
Protein: Q5PRF9 (aka SMAG2_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.