Human Gene SOX11 (ENST00000322002.5_4) from GENCODE V47lift37
  Description: SRY-box transcription factor 11 (from RefSeq NM_003108.4)
Gencode Transcript: ENST00000322002.5_4
Gencode Gene: ENSG00000176887.7_12
Transcript (Including UTRs)
   Position: hg19 chr2:5,832,516-5,841,517 Size: 9,002 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr2:5,832,854-5,834,179 Size: 1,326 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:5,832,516-5,841,517)mRNA (may differ from genome)Protein (441 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX11_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-11;
FUNCTION: Probably important in the developing nervous system. May also have a role in tissue modeling during development.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Expressed mainly in the nervous system.
SIMILARITY: Contains 1 HMG box DNA-binding 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


-  MalaCards Disease Associations
  MalaCards Gene Search: SOX11
Diseases sorted by gene-association score: mental retardation, autosomal dominant, 27* (1330), coffin-siris syndrome 1* (149), prostate lymphoma (16), burkitt lymphoma (10), mantle cell lymphoma (10), charge syndrome (8), chromosome 13q14 deletion syndrome (7), cll/sll (6), composite lymphoma (6), pediatric ependymoma (6)
* = Manually curated disease association

-  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: 1.40 RPKM in Brain - Hypothalamus
Total median expression: 10.38 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -168.40338-0.498 Picture PostScript Text
3' UTR -2355.407338-0.321 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 P35716
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000979 RNA polymerase II core promoter 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:0001158 enhancer sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0008135 translation factor activity, RNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001501 skeletal system development
GO:0001822 kidney development
GO:0001841 neural tube formation
GO:0002089 lens morphogenesis in camera-type eye
GO:0003151 outflow tract morphogenesis
GO:0003211 cardiac ventricle formation
GO:0003357 noradrenergic neuron differentiation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006412 translation
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0014003 oligodendrocyte development
GO:0014009 glial cell proliferation
GO:0014032 neural crest cell development
GO:0017015 regulation of transforming growth factor beta receptor signaling pathway
GO:0021510 spinal cord development
GO:0021782 glial cell development
GO:0030154 cell differentiation
GO:0030182 neuron differentiation
GO:0030513 positive regulation of BMP signaling pathway
GO:0035332 positive regulation of hippo signaling
GO:0035914 skeletal muscle cell differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045669 positive regulation of osteoblast differentiation
GO:0045778 positive regulation of ossification
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046887 positive regulation of hormone secretion
GO:0048485 sympathetic nervous system development
GO:0048557 embryonic digestive tract morphogenesis
GO:0048704 embryonic skeletal system morphogenesis
GO:0050672 negative regulation of lymphocyte proliferation
GO:0050769 positive regulation of neurogenesis
GO:0060022 hard palate development
GO:0060023 soft palate development
GO:0060174 limb bud formation
GO:0060253 negative regulation of glial cell proliferation
GO:0060412 ventricular septum morphogenesis
GO:0060425 lung morphogenesis
GO:0060548 negative regulation of cell death
GO:0060563 neuroepithelial cell differentiation
GO:0061029 eyelid development in camera-type eye
GO:0061053 somite development
GO:0061303 cornea development in camera-type eye
GO:0061386 closure of optic fissure
GO:0072395 signal transduction involved in cell cycle checkpoint
GO:2000648 positive regulation of stem cell proliferation
GO:2000678 negative regulation of transcription regulatory region DNA binding
GO:2001111 positive regulation of lens epithelial cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  U23752 - Human SOX-11 mRNA, complete cds.
AB028641 - Homo sapiens mRNA for SOX11, complete cds.
BC025789 - Homo sapiens SRY (sex determining region Y)-box 11, mRNA (cDNA clone IMAGE:5201591), partial cds.
AB464713 - Synthetic construct DNA, clone: pF1KB9649, Homo sapiens SOX11 gene for SRY (sex determining region Y)-box 11, without stop codon, in Flexi system.
BC160119 - Synthetic construct Homo sapiens clone IMAGE:100064151, MGC:193234 SRY (sex determining region Y)-box 11 (SOX11) mRNA, encodes complete protein.
JD545277 - Sequence 526301 from Patent EP1572962.
JD165405 - Sequence 146429 from Patent EP1572962.
JD545553 - Sequence 526577 from Patent EP1572962.
JD242265 - Sequence 223289 from Patent EP1572962.
JD266666 - Sequence 247690 from Patent EP1572962.
JD416877 - Sequence 397901 from Patent EP1572962.
JD184977 - Sequence 166001 from Patent EP1572962.
JD481831 - Sequence 462855 from Patent EP1572962.
JD300388 - Sequence 281412 from Patent EP1572962.
JD216080 - Sequence 197104 from Patent EP1572962.
JD235294 - Sequence 216318 from Patent EP1572962.
JD329535 - Sequence 310559 from Patent EP1572962.
JD374761 - Sequence 355785 from Patent EP1572962.
JD305552 - Sequence 286576 from Patent EP1572962.
JD229159 - Sequence 210183 from Patent EP1572962.
JD274431 - Sequence 255455 from Patent EP1572962.
JD360873 - Sequence 341897 from Patent EP1572962.
JD297496 - Sequence 278520 from Patent EP1572962.
JD518205 - Sequence 499229 from Patent EP1572962.
JD338017 - Sequence 319041 from Patent EP1572962.
JD120238 - Sequence 101262 from Patent EP1572962.
JD556156 - Sequence 537180 from Patent EP1572962.
JD398468 - Sequence 379492 from Patent EP1572962.
JD422733 - Sequence 403757 from Patent EP1572962.
JD464989 - Sequence 446013 from Patent EP1572962.
JD466116 - Sequence 447140 from Patent EP1572962.
JD408771 - Sequence 389795 from Patent EP1572962.
JD485245 - Sequence 466269 from Patent EP1572962.
JD261137 - Sequence 242161 from Patent EP1572962.
JD467137 - Sequence 448161 from Patent EP1572962.
JD119144 - Sequence 100168 from Patent EP1572962.
JD462895 - Sequence 443919 from Patent EP1572962.
JD408208 - Sequence 389232 from Patent EP1572962.
JD481695 - Sequence 462719 from Patent EP1572962.
JD043276 - Sequence 24300 from Patent EP1572962.
JD445614 - Sequence 426638 from Patent EP1572962.
JD226506 - Sequence 207530 from Patent EP1572962.
JD293789 - Sequence 274813 from Patent EP1572962.
JD151187 - Sequence 132211 from Patent EP1572962.
JD408768 - Sequence 389792 from Patent EP1572962.
JD139860 - Sequence 120884 from Patent EP1572962.
JD109042 - Sequence 90066 from Patent EP1572962.
JD485678 - Sequence 466702 from Patent EP1572962.
JD129950 - Sequence 110974 from Patent EP1572962.
JD433263 - Sequence 414287 from Patent EP1572962.
JD466661 - Sequence 447685 from Patent EP1572962.
JD104549 - Sequence 85573 from Patent EP1572962.
JD407230 - Sequence 388254 from Patent EP1572962.
JD434523 - Sequence 415547 from Patent EP1572962.
JD554926 - Sequence 535950 from Patent EP1572962.
JD460225 - Sequence 441249 from Patent EP1572962.
JD129795 - Sequence 110819 from Patent EP1572962.
JD115925 - Sequence 96949 from Patent EP1572962.
JD482301 - Sequence 463325 from Patent EP1572962.
JD231330 - Sequence 212354 from Patent EP1572962.
JD548686 - Sequence 529710 from Patent EP1572962.
JD490772 - Sequence 471796 from Patent EP1572962.
JD315676 - Sequence 296700 from Patent EP1572962.
JD307702 - Sequence 288726 from Patent EP1572962.
JD058648 - Sequence 39672 from Patent EP1572962.
JD222438 - Sequence 203462 from Patent EP1572962.
JD040899 - Sequence 21923 from Patent EP1572962.
JD037536 - Sequence 18560 from Patent EP1572962.
JD469271 - Sequence 450295 from Patent EP1572962.
JD357491 - Sequence 338515 from Patent EP1572962.
JD349616 - Sequence 330640 from Patent EP1572962.
JD433022 - Sequence 414046 from Patent EP1572962.
JD285226 - Sequence 266250 from Patent EP1572962.
JD506740 - Sequence 487764 from Patent EP1572962.
JD357383 - Sequence 338407 from Patent EP1572962.
JD093568 - Sequence 74592 from Patent EP1572962.
JD037425 - Sequence 18449 from Patent EP1572962.
JD300139 - Sequence 281163 from Patent EP1572962.
JD507977 - Sequence 489001 from Patent EP1572962.
JD048815 - Sequence 29839 from Patent EP1572962.
JD430651 - Sequence 411675 from Patent EP1572962.
JD506730 - Sequence 487754 from Patent EP1572962.
JD289393 - Sequence 270417 from Patent EP1572962.
JD476518 - Sequence 457542 from Patent EP1572962.
JD303482 - Sequence 284506 from Patent EP1572962.
JD442058 - Sequence 423082 from Patent EP1572962.
JD490688 - Sequence 471712 from Patent EP1572962.
JD345193 - Sequence 326217 from Patent EP1572962.
JD504721 - Sequence 485745 from Patent EP1572962.
MA872516 - JP 2018536436-A/4352: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY594928 - KR 1020180133840-A/4352: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000322002.1, ENST00000322002.2, ENST00000322002.3, ENST00000322002.4, NM_003108, P35716, Q4ZFV8, SOX11_HUMAN, uc317rek.1, uc317rek.2
UCSC ID: ENST00000322002.5_4
RefSeq Accession: NM_003108.4
Protein: P35716 (aka SOX11_HUMAN or SX11_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SOX11:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
coffin-siris (Coffin-Siris Syndrome)

-  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.