Human Gene SHF (uc001zuy.3)
  Description: Homo sapiens Src homology 2 domain containing F (SHF), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr15:45,459,412-45,493,373 Size: 33,962 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr15:45,460,145-45,491,272 Size: 31,128 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:45,459,412-45,493,373)mRNA (may differ from genome)Protein (423 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SHF_HUMAN
DESCRIPTION: RecName: Full=SH2 domain-containing adapter protein F;
FUNCTION: Adapter protein which may play a role in the regulation of apoptosis in response to PDGF.
SUBUNIT: Interacts with phosphorylated 'Tyr-720' of PDGFRA via its SH2 domain.
TISSUE SPECIFICITY: Expressed in skeletal muscle, brain, liver, prostate, testis, ovary, small intestine and colon.
PTM: May become phosphorylated upon binding to PDGFRA.
MISCELLANEOUS: The sequence described in PubMed:11095946 is over- extended by 57 aa at the N-terminus due to the presence of an uncorrected 5' mismatch compared to the reference genome sequence.
SIMILARITY: Contains 1 SH2 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SHF
CDC HuGE Published Literature: SHF
Positive Disease Associations: Hemoglobin A, Glycosylated , Stroke , Uric Acid
Related Studies:
  1. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  2. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  3. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • D010634 Phenobarbital

+  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: 39.65 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 170.01 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 -157.82495-0.319 Picture PostScript Text
3' UTR -343.30733-0.468 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
IPR000980 - SH2

Pfam Domains:
PF00017 - SH2 domain

SCOP Domains:
52374 - Nucleotidylyl transferase
55550 - SH2 domain

ModBase Predicted Comparative 3D Structure on Q7M4L6
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005070 SH3/SH2 adaptor activity

Biological Process:
GO:0006915 apoptotic process
GO:0007165 signal transduction
GO:0009967 positive regulation of signal transduction


-  Descriptions from all associated GenBank mRNAs
  AK096267 - Homo sapiens cDNA FLJ38948 fis, clone NT2NE2018165, weakly similar to SH2 domain-containing adapter protein E.
AB528975 - Synthetic construct DNA, clone: pF1KE0736, Homo sapiens SHF gene for Src homology 2 domain containing protein F, without stop codon, in Flexi system.
BC007586 - Homo sapiens Src homology 2 domain containing F, mRNA (cDNA clone IMAGE:3162799), partial cds.
KY994050 - Homo sapiens QXBT8 miRNA, complete sequence.
KY994072 - Homo sapiens precursor microRNA QXBT8, complete sequence.
JD468435 - Sequence 449459 from Patent EP1572962.
JD103287 - Sequence 84311 from Patent EP1572962.
AK301625 - Homo sapiens cDNA FLJ54190 complete cds, moderately similar to SH2 domain-containing adapter protein B.
JD494024 - Sequence 475048 from Patent EP1572962.
AK303749 - Homo sapiens cDNA FLJ56331 complete cds, weakly similar to SH2 domain-containing adapter protein B.
AK123658 - Homo sapiens cDNA FLJ41664 fis, clone FEBRA2027352.
AK094391 - Homo sapiens cDNA FLJ37072 fis, clone BRACE2015412, weakly similar to Shb=Src homology 2 protein.
BC101601 - Homo sapiens Src homology 2 domain containing F, mRNA (cDNA clone MGC:126650 IMAGE:8069107), complete cds.
BC143601 - Homo sapiens Src homology 2 domain containing F, mRNA (cDNA clone IMAGE:9052113), partial cds.
BC171730 - Homo sapiens Src homology 2 domain containing F, mRNA (cDNA clone IMAGE:9052114), partial cds.
BC101603 - Homo sapiens Src homology 2 domain containing F, mRNA (cDNA clone MGC:126652 IMAGE:8069109), complete cds.
KJ904941 - Synthetic construct Homo sapiens clone ccsbBroadEn_14335 SHF-like gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_138356, NP_612365, Q7M4L6, Q96IE8, SHF_HUMAN
UCSC ID: uc001zuy.3
RefSeq Accession: NM_138356
Protein: Q7M4L6 (aka SHF_HUMAN)
CCDS: CCDS10120.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138356.2
exon count: 8CDS single in 3' UTR: no RNA size: 2517
ORF size: 1272CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 2392.00frame shift in genome: no % Coverage: 99.32
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.