Human Gene SOX12 (uc002wdh.4) Description and Page Index
  Description: Homo sapiens SRY (sex determining region Y)-box 12 (SOX12), mRNA.
RefSeq Summary (NM_006943): Members of the SOX family of transcription factors are characterized by the presence of a DNA-binding high mobility group (HMG) domain, homologous to the HMG box of sex-determining region Y (SRY). Forming a subgroup of the HMG domain superfamily, SOX proteins have been implicated in cell fate decisions in a diverse range of developmental processes. SOX transcription factors have diverse tissue-specific expression patterns during early development and have been proposed to act as target-specific transcription factors and/or as chromatin structure regulatory elements. The protein encoded by this gene was identified as a SOX family member based on conserved domains, and its expression in various tissues suggests a role in both differentiation and maintenance of several cell types. [provided by RefSeq, Jan 2013]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr20:306,215-310,872 Size: 4,658 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr20:306,569-307,516 Size: 948 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:306,215-310,872)mRNA (may differ from genome)Protein (315 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SOX12_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-12; AltName: Full=Protein SOX-22;
FUNCTION: Binds to the sequence 5'-AACAAT-3' (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed most abundantly in the CNS. Also expressed in fetal brain and kidney and adult heart, pancreas, testis and ovary. Other tissues were only weakly positive.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAB69627.1; Type=Frameshift; Positions=135, 201;

-  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: 12.80 RPKM in Brain - Cerebellum
Total median expression: 262.18 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -204.66354-0.578 Picture PostScript Text
3' UTR -1324.813356-0.395 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
IPR017386 - SOX-12/11/4a

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

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on O15370
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 orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
  Ensembl  SGD
  Protein Sequence  Protein Sequence
  Alignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003677 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:0006366 transcription from RNA polymerase II promoter
GO:0021510 spinal cord development
GO:0045165 cell fate commitment
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0065004 protein-DNA complex assembly

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0032993 protein-DNA complex


-  Descriptions from all associated GenBank mRNAs
  KJ892188 - Synthetic construct Homo sapiens clone ccsbBroadEn_01582 SOX12 gene, encodes complete protein.
BC067361 - Homo sapiens SRY (sex determining region Y)-box 12, mRNA (cDNA clone MGC:71161 IMAGE:6480102), complete cds.
JD129603 - Sequence 110627 from Patent EP1572962.
U35612 - Homo sapiens SOX22 protein (SOX22) mRNA, complete cds.
BC028103 - Homo sapiens, clone IMAGE:5243032, mRNA.
JD125223 - Sequence 106247 from Patent EP1572962.
JD090698 - Sequence 71722 from Patent EP1572962.
JD408439 - Sequence 389463 from Patent EP1572962.
JD128800 - Sequence 109824 from Patent EP1572962.
JD407369 - Sequence 388393 from Patent EP1572962.
JD171462 - Sequence 152486 from Patent EP1572962.
JD416380 - Sequence 397404 from Patent EP1572962.
JD124923 - Sequence 105947 from Patent EP1572962.
JD103144 - Sequence 84168 from Patent EP1572962.
JD389696 - Sequence 370720 from Patent EP1572962.
JD361407 - Sequence 342431 from Patent EP1572962.
JD191448 - Sequence 172472 from Patent EP1572962.
JD397517 - Sequence 378541 from Patent EP1572962.
JD439716 - Sequence 420740 from Patent EP1572962.
JD238872 - Sequence 219896 from Patent EP1572962.
JD139755 - Sequence 120779 from Patent EP1572962.
JD304878 - Sequence 285902 from Patent EP1572962.
JD199894 - Sequence 180918 from Patent EP1572962.
JD139877 - Sequence 120901 from Patent EP1572962.
JD538739 - Sequence 519763 from Patent EP1572962.
JD439287 - Sequence 420311 from Patent EP1572962.
JD222854 - Sequence 203878 from Patent EP1572962.
JD212318 - Sequence 193342 from Patent EP1572962.
JD050424 - Sequence 31448 from Patent EP1572962.
JD180637 - Sequence 161661 from Patent EP1572962.
JD158515 - Sequence 139539 from Patent EP1572962.
JD232044 - Sequence 213068 from Patent EP1572962.
JD279630 - Sequence 260654 from Patent EP1572962.
JD280742 - Sequence 261766 from Patent EP1572962.
JD287013 - Sequence 268037 from Patent EP1572962.
JD469553 - Sequence 450577 from Patent EP1572962.
JD466258 - Sequence 447282 from Patent EP1572962.
JD337935 - Sequence 318959 from Patent EP1572962.
JD373493 - Sequence 354517 from Patent EP1572962.
JD076734 - Sequence 57758 from Patent EP1572962.
JD276493 - Sequence 257517 from Patent EP1572962.
JD409083 - Sequence 390107 from Patent EP1572962.
JD548666 - Sequence 529690 from Patent EP1572962.
JD419942 - Sequence 400966 from Patent EP1572962.
JD531296 - Sequence 512320 from Patent EP1572962.
JD397611 - Sequence 378635 from Patent EP1572962.
JD249310 - Sequence 230334 from Patent EP1572962.
JD252659 - Sequence 233683 from Patent EP1572962.
JD384908 - Sequence 365932 from Patent EP1572962.
JD174591 - Sequence 155615 from Patent EP1572962.
JD182159 - Sequence 163183 from Patent EP1572962.
JD157296 - Sequence 138320 from Patent EP1572962.
JD287005 - Sequence 268029 from Patent EP1572962.
JD197503 - Sequence 178527 from Patent EP1572962.
JD476073 - Sequence 457097 from Patent EP1572962.
JD387250 - Sequence 368274 from Patent EP1572962.
JD477390 - Sequence 458414 from Patent EP1572962.
JD400276 - Sequence 381300 from Patent EP1572962.
JD133455 - Sequence 114479 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006943, NP_008874, O15370, Q5D038, Q9NUD4, SOX12_HUMAN, SOX22, uc002wdh.3
UCSC ID: uc002wdh.4
RefSeq Accession: NM_006943
Protein: O15370 (aka SOX12_HUMAN or SX12_HUMAN)
CCDS: CCDS12995.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006943.3
exon count: 1CDS single in 3' UTR: no RNA size: 4658
ORF size: 948CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1760.00frame shift in genome: no % Coverage: 100.00
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.