Human Gene SOX30 (uc003lxb.1) Description and Page Index
  Description: Homo sapiens SRY (sex determining region Y)-box 30 (SOX30), transcript variant 1, mRNA.
RefSeq Summary (NM_178424): This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein acts as a transcriptional regulator when present in a complex with other proteins. It can activate p53 transcription to promote tumor cell apoptosis in lung cancer. The protein may be involved in the differentiation of developing male germ cells. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Apr 2015].
Transcript (Including UTRs)
   Position: hg19 chr5:157,052,687-157,079,428 Size: 26,742 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr5:157,053,348-157,079,086 Size: 25,739 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:157,052,687-157,079,428)mRNA (may differ from genome)Protein (753 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SOX30_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-30;
FUNCTION: Transcriptional activator. Binds to the DNA sequence 5'- ACAAT-3' and shows a preference for guanine residues surrounding this core motif.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in testis.
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SOX30
CDC HuGE Published Literature: SOX30
Positive Disease Associations: Respiratory Function Tests
Related Studies:
  1. Respiratory Function Tests
    Jemma B Wilk et al. BMC medical genetics 2007, Framingham Heart Study genome-wide association: results for pulmonary function measures., BMC medical genetics. [PubMed 17903307]
    GSTO2 and IL6R are credible candidate genes for association to pulmonary function identified by GWA. These and other observed associations warrant replication studies. This resource of GWA results for pulmonary function measures is publicly available at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.

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

+  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: 64.15 RPKM in Testis
Total median expression: 66.72 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 -133.90342-0.392 Picture PostScript Text
3' UTR -131.36661-0.199 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
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on O94993
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007283 spermatogenesis
GO:0031960 response to corticosteroid

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AB022083 - Homo sapiens mRNA for SOX30 protein, complete cds.
AB022441 - Homo sapiens mRNA for Sox30 protein typeII, complete cds.
JD562983 - Sequence 544007 from Patent EP1572962.
JD172616 - Sequence 153640 from Patent EP1572962.
JD379019 - Sequence 360043 from Patent EP1572962.
JD281536 - Sequence 262560 from Patent EP1572962.
AK302162 - Homo sapiens cDNA FLJ53881 complete cds, highly similar to Transcription factor SOX-30.
AK308329 - Homo sapiens cDNA, FLJ98277.
BC033492 - Homo sapiens SRY (sex determining region Y)-box 30, mRNA (cDNA clone MGC:34408 IMAGE:5172577), complete cds.
AK225861 - Homo sapiens mRNA for SRY-box 30 isoform a variant, clone: FCC125A11.
JD471141 - Sequence 452165 from Patent EP1572962.
AB527685 - Synthetic construct DNA, clone: pF1KB6245, Homo sapiens SOX30 gene for SRY (sex determining region Y)-box 30, without stop codon, in Flexi system.
JD067331 - Sequence 48355 from Patent EP1572962.
JD069086 - Sequence 50110 from Patent EP1572962.
JD539760 - Sequence 520784 from Patent EP1572962.
JD435875 - Sequence 416899 from Patent EP1572962.
JD240665 - Sequence 221689 from Patent EP1572962.
JD219376 - Sequence 200400 from Patent EP1572962.
JD229241 - Sequence 210265 from Patent EP1572962.
JD477909 - Sequence 458933 from Patent EP1572962.
JD042962 - Sequence 23986 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_178424, NP_848511, O94993, O94995, Q8IYX6, SOX30_HUMAN
UCSC ID: uc003lxb.1
RefSeq Accession: NM_178424
Protein: O94993 (aka SOX30_HUMAN or SX30_HUMAN)
CCDS: CCDS4339.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178424.1
exon count: 5CDS single in 3' UTR: no RNA size: 3280
ORF size: 2262CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3906.00frame shift in genome: no % Coverage: 99.54
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.