Human Gene SAMD4A (ENST00000554335.6_11) from GENCODE V47lift37
  Description: sterile alpha motif domain containing 4A, transcript variant 1 (from RefSeq NM_015589.6)
Gencode Transcript: ENST00000554335.6_11
Gencode Gene: ENSG00000020577.14_14
Transcript (Including UTRs)
   Position: hg19 chr14:55,033,846-55,260,030 Size: 226,185 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr14:55,034,635-55,255,662 Size: 221,028 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:55,033,846-55,260,030)mRNA (may differ from genome)Protein (718 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SMAG1_HUMAN
DESCRIPTION: RecName: Full=Protein Smaug homolog 1; Short=Smaug 1; Short=hSmaug1; AltName: Full=Sterile alpha motif domain-containing protein 4A; Short=SAM domain-containing protein 4A;
FUNCTION: Acts as a translational repressor of SRE-containing messengers.
SUBCELLULAR LOCATION: Cytoplasm. Cell projection, dendrite (By similarity). Cell junction, synapse, synaptosome (By similarity). Note=Enriched in synaptoneurosomes (By similarity). Shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner. Colocalizes throughout the cytoplasm in granules with polyadenylated RNAs, PABPC1 and STAU1. Also frequently colocalizes in cytoplasmic stress granule-like foci with ELAVL1, TIA1 and TIAL1.
SIMILARITY: Belongs to the SMAUG family.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.
SEQUENCE CAUTION: Sequence=AAH57838.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=AAP97302.1; Type=Miscellaneous discrepancy; Note=Intron retention;

-  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           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: 38.55 RPKM in Testis
Total median expression: 410.12 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 -277.30632-0.439 Picture PostScript Text
3' UTR -1307.404368-0.299 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)

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q9UPU9
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 DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0030371 translation repressor activity

Biological Process:
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
GO:0006417 regulation of translation
GO:0017148 negative regulation of translation
GO:0043488 regulation of mRNA stability
GO:0045727 positive regulation of translation

Cellular Component:
GO:0000932 P-body
GO:0001650 fibrillar center
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030054 cell junction
GO:0030425 dendrite
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  BC057838 - Homo sapiens sterile alpha motif domain containing 4A, mRNA (cDNA clone IMAGE:30345653), complete cds.
CU691270 - Synthetic construct Homo sapiens gateway clone IMAGE:100021091 5' read SAMD4A mRNA.
KJ902268 - Synthetic construct Homo sapiens clone ccsbBroadEn_11662 SAMD4A gene, encodes complete protein.
BC121173 - Homo sapiens sterile alpha motif domain containing 4A, mRNA (cDNA clone MGC:150558 IMAGE:40122465), complete cds.
BC121174 - Homo sapiens sterile alpha motif domain containing 4A, mRNA (cDNA clone MGC:150559 IMAGE:40122467), complete cds.
AK024652 - Homo sapiens cDNA: FLJ20999 fis, clone CAE03237.
KJ898437 - Synthetic construct Homo sapiens clone ccsbBroadEn_07831 SAMD4A gene, encodes complete protein.
BX648198 - Homo sapiens mRNA; cDNA DKFZp686A1532 (from clone DKFZp686A1532).
AB028976 - Homo sapiens mRNA for KIAA1053 protein, partial cds.
AK025923 - Homo sapiens cDNA: FLJ22270 fis, clone HRC03189.
AF429970 - Homo sapiens hypothetical protein mRNA, complete cds.
BC021060 - Homo sapiens sterile alpha motif domain containing 4A, mRNA (cDNA clone IMAGE:2967815).
BC021726 - Homo sapiens sterile alpha motif domain containing 4A, mRNA (cDNA clone IMAGE:4829743), partial cds.
CU692398 - Synthetic construct Homo sapiens gateway clone IMAGE:100019035 5' read SAMD4A mRNA.
KJ906077 - Synthetic construct Homo sapiens clone ccsbBroadEn_15747 SAMD4A gene, encodes complete protein.
AL117523 - Homo sapiens mRNA; cDNA DKFZp434H0350 (from clone DKFZp434H0350).
JD021642 - Sequence 2666 from Patent EP1572962.
LF210032 - JP 2014500723-A/17535: Polycomb-Associated Non-Coding RNAs.
LF334173 - JP 2014500723-A/141676: Polycomb-Associated Non-Coding RNAs.
LF334174 - JP 2014500723-A/141677: Polycomb-Associated Non-Coding RNAs.
AK074716 - Homo sapiens cDNA FLJ90235 fis, clone NT2RM2000582.
LF334175 - JP 2014500723-A/141678: Polycomb-Associated Non-Coding RNAs.
LF334176 - JP 2014500723-A/141679: Polycomb-Associated Non-Coding RNAs.
LF334177 - JP 2014500723-A/141680: Polycomb-Associated Non-Coding RNAs.
BC011489 - Homo sapiens cDNA clone IMAGE:4152923, partial cds.
LF334178 - JP 2014500723-A/141681: Polycomb-Associated Non-Coding RNAs.
MA445609 - JP 2018138019-A/17535: Polycomb-Associated Non-Coding RNAs.
MA569750 - JP 2018138019-A/141676: Polycomb-Associated Non-Coding RNAs.
MA569751 - JP 2018138019-A/141677: Polycomb-Associated Non-Coding RNAs.
MA569752 - JP 2018138019-A/141678: Polycomb-Associated Non-Coding RNAs.
MA569753 - JP 2018138019-A/141679: Polycomb-Associated Non-Coding RNAs.
MA569754 - JP 2018138019-A/141680: Polycomb-Associated Non-Coding RNAs.
MA569755 - JP 2018138019-A/141681: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8MPZ5, ENST00000554335.1, ENST00000554335.2, ENST00000554335.3, ENST00000554335.4, ENST00000554335.5, KIAA1053, NM_015589, Q0VA96, Q6PEW4, Q9UPU9, SAMD4, SMAG1_HUMAN, SMAUG1, uc325ftg.1, uc325ftg.2
UCSC ID: ENST00000554335.6_11
RefSeq Accession: NM_015589.6
Protein: Q9UPU9 (aka SMAG1_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.