Human Gene SON (ENST00000436227.5) from GENCODE V44
  Description: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data. (from UniProt H7C1M2)
RefSeq Summary (NR_103797): This gene encodes a protein that contains multiple simple repeats. The encoded protein binds RNA and promotes pre-mRNA splicing, particularly of transcripts with poor splice sites. The protein also recognizes a specific DNA sequence found in the human hepatitis B virus (HBV) and represses HBV core promoter activity. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013].
Gencode Transcript: ENST00000436227.5
Gencode Gene: ENSG00000159140.23
Transcript (Including UTRs)
   Position: hg38 chr21:33,552,248-33,577,481 Size: 25,234 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr21:33,552,248-33,576,576 Size: 24,329 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:33,552,248-33,577,481)mRNA (may differ from genome)Protein (1452 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGImyGene2PubMedUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: H7C1M2_HUMAN
DESCRIPTION: SubName: Full=Protein SON; Flags: Fragment;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: SON
Diseases sorted by gene-association score: zttk syndrome* (928), blue color blindness (12), lethal congenital contracture syndrome 1 (10), anterior horn cell disease (9), glossopharyngeal neuralgia (9), glossopharyngeal nerve disease (9), hepatitis b (5), intellectual disability (2)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 41.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1226.45 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
3' UTR -214.00905-0.236 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
IPR001159 - Ds-RNA-bd
IPR014720 - dsRNA-bd-like
IPR000467 - G_patch_dom

Pfam Domains:
PF00035 - Double-stranded RNA binding motif
PF01585 - G-patch domain

ModBase Predicted Comparative 3D Structure on H7C1M2
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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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0043484 regulation of RNA splicing
GO:0051726 regulation of cell cycle

Cellular Component:
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK307612 - Homo sapiens cDNA, FLJ97560.
AY026895 - Homo sapiens NREBP mRNA, complete cds.
AK127947 - Homo sapiens cDNA FLJ46057 fis, clone T1ESE2000609, highly similar to SON protein.
AF380180 - Homo sapiens SON DNA binding protein isoform B (SON) mRNA, complete cds, alternatively spliced.
AF380179 - Homo sapiens SON DNA binding protein isoform A (SON) mRNA, complete cds, alternatively spliced.
AF380181 - Homo sapiens SON DNA binding protein isoform C (SON) mRNA, complete cds, alternatively spliced.
AF380183 - Homo sapiens SON DNA binding protein isoform E (SON) mRNA, complete cds, alternatively spliced.
AF380184 - Homo sapiens SON DNA binding protein isoform F (SON) mRNA, complete cds, alternatively spliced.
AB028942 - Homo sapiens KIAA1019 mRNA for KIAA1019 protein.
BC046101 - Homo sapiens SON DNA binding protein, mRNA (cDNA clone IMAGE:5552607), containing frame-shift errors.
AK091233 - Homo sapiens cDNA FLJ33914 fis, clone CTONG2016575, highly similar to SON PROTEIN.
AX746865 - Sequence 390 from Patent EP1308459.
AK074269 - Homo sapiens cDNA FLJ23689 fis, clone HEP10174, highly similar to SON PROTEIN.
AK128071 - Homo sapiens cDNA FLJ46192 fis, clone TESTI4005653, moderately similar to Homo sapiens SON DNA binding protein (SON).
BC002422 - Homo sapiens SON DNA binding protein, mRNA (cDNA clone IMAGE:3161999), partial cds.
X63753 - Homo sapiens son-a mRNA.
X63751 - Homo sapiens mRNA for putative DNA binding protein (son-b).
X63071 - H.sapiens mRNA for novel DNA binding protein.
BC017278 - Homo sapiens cDNA clone IMAGE:4853468, partial cds.
AF435977 - Homo sapiens negative regulatory element-binding protein (SON) mRNA, complete cds, alternatively spliced.
LF210669 - JP 2014500723-A/18172: Polycomb-Associated Non-Coding RNAs.
MA446246 - JP 2018138019-A/18172: Polycomb-Associated Non-Coding RNAs.
LF339913 - JP 2014500723-A/147416: Polycomb-Associated Non-Coding RNAs.
MA575490 - JP 2018138019-A/147416: Polycomb-Associated Non-Coding RNAs.
AF139897 - Homo sapiens BASS1 (BASS1) mRNA, partial cds.
JD310635 - Sequence 291659 from Patent EP1572962.
JD502446 - Sequence 483470 from Patent EP1572962.
JD535242 - Sequence 516266 from Patent EP1572962.
JD280558 - Sequence 261582 from Patent EP1572962.
JD377491 - Sequence 358515 from Patent EP1572962.
JD348624 - Sequence 329648 from Patent EP1572962.
AF380182 - Homo sapiens SON DNA binding protein isoform D (SON) mRNA, complete cds, alternatively spliced.
JD278510 - Sequence 259534 from Patent EP1572962.
JD557759 - Sequence 538783 from Patent EP1572962.
JD130157 - Sequence 111181 from Patent EP1572962.
JD297016 - Sequence 278040 from Patent EP1572962.
JD503410 - Sequence 484434 from Patent EP1572962.
JD385345 - Sequence 366369 from Patent EP1572962.
JD108762 - Sequence 89786 from Patent EP1572962.
JD225016 - Sequence 206040 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AF380179, ENST00000436227.1, ENST00000436227.2, ENST00000436227.3, ENST00000436227.4, H7C1M2, H7C1M2_HUMAN, uc061zrh.1
UCSC ID: ENST00000436227.5
RefSeq Accession: NR_103797
Protein: H7C1M2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.