Human Gene SPEN (ENST00000375759.8_4) from GENCODE V47lift37
  Description: spen family transcriptional repressor (from RefSeq NM_015001.3)
Gencode Transcript: ENST00000375759.8_4
Gencode Gene: ENSG00000065526.13_14
Transcript (Including UTRs)
   Position: hg19 chr1:16,174,202-16,266,951 Size: 92,750 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr1:16,174,563-16,265,922 Size: 91,360 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:16,174,202-16,266,951)mRNA (may differ from genome)Protein (3664 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MINT_HUMAN
DESCRIPTION: RecName: Full=Msx2-interacting protein; AltName: Full=SMART/HDAC1-associated repressor protein; AltName: Full=SPEN homolog;
FUNCTION: May serve as a nuclear matrix platform that organizes and integrates transcriptional responses. In osteoblasts, supports transcription activation: synergizes with RUNX2 to enhance FGFR2- mediated activation of the osteocalcin FGF-responsive element (OCFRE) (By similarity). Has also been shown to be an essential corepressor protein, which probably regulates different key pathways such as the Notch pathway. Negative regulator of the Notch pathway via its interaction with RBPSUH, which prevents the association between NOTCH1 and RBPSUH, and therefore suppresses the transactivation activity of Notch signaling. Blocks the differentiation of precursor B-cells into marginal zone B-cells. Probably represses transcription via the recruitment of large complexes containing histone deacetylase proteins. May bind both to DNA and RNA.
SUBUNIT: Interacts with MSX2 and HIPK3 (By similarity). Interacts with NCOR2, HDAC1, HDAC2, RBBP4, MBD3 and MTA1L1. Interacts with RBPSUH; this interaction may prevent the interaction between RBPSUH and NOTCH1. Interacts with the nuclear receptors RAR and PPARD. Interacts with RAR in absence of ligand. Binds to the steroid receptor RNA coactivator SRA. Interacts with Epstein-Barr virus BSFL2/BMLF1.
INTERACTION: P16333:NCK1; NbExp=3; IntAct=EBI-765739, EBI-389883;
SUBCELLULAR LOCATION: Nucleus. Note=Associates with chromatin.
TISSUE SPECIFICITY: Expressed at high level in brain, testis, spleen and thymus. Expressed at intermediate level in kidney, liver, mammary gland and skin.
INDUCTION: By 17-beta-estradiol.
DOMAIN: The RID domain mediates the interaction with nuclear receptors (By similarity).
DOMAIN: The SPOC domain, which mediates the interaction with NCOR2, is essential for the repressive activity.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the RRM Spen family.
SIMILARITY: Contains 1 RID (receptor interacting) domain.
SIMILARITY: Contains 4 RRM (RNA recognition motif) domains.
SIMILARITY: Contains 1 SPOC domain.
SEQUENCE CAUTION: Sequence=BAA91405.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14324.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAB51072.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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: SPEN
Diseases sorted by gene-association score: lip disease (16), endocervicitis (11), median arcuate ligament syndrome (9), acneiform dermatitis (7), pancreatic cystadenoma (6)

-  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: 18.58 RPKM in Brain - Cerebellum
Total median expression: 530.88 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 -194.70361-0.539 Picture PostScript Text
3' UTR -276.601029-0.269 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR016194 - SPOC-like
IPR012921 - SPOC_C
IPR010912 - SPOC_met

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF07744 - SPOC domain
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
100939 - SPOC domain-like
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1OW1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96T58
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 DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001085 RNA polymerase II transcription factor binding
GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007219 Notch signaling pathway
GO:0016032 viral process
GO:0045892 negative regulation of transcription, DNA-templated
GO:0050769 positive regulation of neurogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0017053 transcriptional repressor complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF356524 - Homo sapiens nuclear receptor transcription cofactor (SHARP) mRNA, complete cds.
BC172877 - Synthetic construct Homo sapiens clone IMAGE:9094453 spen homolog, transcriptional regulator (SPEN) gene, partial cds.
AB384544 - Synthetic construct DNA, clone: pF1KA0929, Homo sapiens SPEN gene for spen homolog, transcriptional regulator, complete cds, without stop codon, in Flexi system.
AK127577 - Homo sapiens cDNA FLJ45672 fis, clone D9OST2003106, highly similar to Homo sapiens SMART/HDAC1 associated repressor protein (SHARP).
AL096858 - Novel human gene mapping to chomosome 1.
AK092332 - Homo sapiens cDNA FLJ35013 fis, clone OCBBF2013789, highly similar to Mus musculus Msx2 interacting nuclear target protein mRNA.
AF085964 - Homo sapiens full length insert cDNA clone YS15G06.
JD460824 - Sequence 441848 from Patent EP1572962.
JD138123 - Sequence 119147 from Patent EP1572962.
JD458582 - Sequence 439606 from Patent EP1572962.
JD056222 - Sequence 37246 from Patent EP1572962.
JD458232 - Sequence 439256 from Patent EP1572962.
JD404652 - Sequence 385676 from Patent EP1572962.
JD187226 - Sequence 168250 from Patent EP1572962.
JD187227 - Sequence 168251 from Patent EP1572962.
JD458449 - Sequence 439473 from Patent EP1572962.
JD436935 - Sequence 417959 from Patent EP1572962.
JD310297 - Sequence 291321 from Patent EP1572962.
JD261410 - Sequence 242434 from Patent EP1572962.
JD304994 - Sequence 286018 from Patent EP1572962.
JD254890 - Sequence 235914 from Patent EP1572962.
JD448035 - Sequence 429059 from Patent EP1572962.
JD395317 - Sequence 376341 from Patent EP1572962.
JD493216 - Sequence 474240 from Patent EP1572962.
JD525576 - Sequence 506600 from Patent EP1572962.
JD416652 - Sequence 397676 from Patent EP1572962.
JD519482 - Sequence 500506 from Patent EP1572962.
JD392071 - Sequence 373095 from Patent EP1572962.
JD463015 - Sequence 444039 from Patent EP1572962.
AK022949 - Homo sapiens cDNA FLJ12887 fis, clone NT2RP2004066, moderately similar to Mus musculus Msx2 interacting nuclear target protein mRNA.
JD102299 - Sequence 83323 from Patent EP1572962.
JD502516 - Sequence 483540 from Patent EP1572962.
JD324655 - Sequence 305679 from Patent EP1572962.
JD368153 - Sequence 349177 from Patent EP1572962.
JD393046 - Sequence 374070 from Patent EP1572962.
JD073348 - Sequence 54372 from Patent EP1572962.
JD530650 - Sequence 511674 from Patent EP1572962.
JD469043 - Sequence 450067 from Patent EP1572962.
JD436652 - Sequence 417676 from Patent EP1572962.
JD068390 - Sequence 49414 from Patent EP1572962.
JD346790 - Sequence 327814 from Patent EP1572962.
JD333621 - Sequence 314645 from Patent EP1572962.
JD183531 - Sequence 164555 from Patent EP1572962.
AK000882 - Homo sapiens cDNA FLJ10020 fis, clone HEMBA1000555.
JD036723 - Sequence 17747 from Patent EP1572962.
JD369007 - Sequence 350031 from Patent EP1572962.
JD429024 - Sequence 410048 from Patent EP1572962.
BC172878 - Synthetic construct Homo sapiens clone IMAGE:9094454 spen homolog, transcriptional regulator (SPEN) gene, partial cds.
JD181324 - Sequence 162348 from Patent EP1572962.
JD369110 - Sequence 350134 from Patent EP1572962.
JD202685 - Sequence 183709 from Patent EP1572962.
JD094316 - Sequence 75340 from Patent EP1572962.
JD349293 - Sequence 330317 from Patent EP1572962.
JD303953 - Sequence 284977 from Patent EP1572962.
JD289670 - Sequence 270694 from Patent EP1572962.
JD503077 - Sequence 484101 from Patent EP1572962.
JD305001 - Sequence 286025 from Patent EP1572962.
JD317346 - Sequence 298370 from Patent EP1572962.
JD263523 - Sequence 244547 from Patent EP1572962.
JD298840 - Sequence 279864 from Patent EP1572962.
JD433656 - Sequence 414680 from Patent EP1572962.
JD317657 - Sequence 298681 from Patent EP1572962.
JD186934 - Sequence 167958 from Patent EP1572962.
JD352315 - Sequence 333339 from Patent EP1572962.
JD329327 - Sequence 310351 from Patent EP1572962.
JD038266 - Sequence 19290 from Patent EP1572962.
JD287600 - Sequence 268624 from Patent EP1572962.
JD247977 - Sequence 229001 from Patent EP1572962.
JD122506 - Sequence 103530 from Patent EP1572962.
JD076297 - Sequence 57321 from Patent EP1572962.
JD461736 - Sequence 442760 from Patent EP1572962.
JD221329 - Sequence 202353 from Patent EP1572962.
JD490806 - Sequence 471830 from Patent EP1572962.
JD503421 - Sequence 484445 from Patent EP1572962.
AB023146 - Homo sapiens mRNA for KIAA0929 protein, partial cds.
BC172907 - Synthetic construct Homo sapiens clone IMAGE:9094483 spen homolog, transcriptional regulator (SPEN) gene, partial cds.
DQ585970 - Homo sapiens piRNA piR-53082, complete sequence.
JD066225 - Sequence 47249 from Patent EP1572962.
JD188712 - Sequence 169736 from Patent EP1572962.
JD136509 - Sequence 117533 from Patent EP1572962.
JD109432 - Sequence 90456 from Patent EP1572962.
JD109044 - Sequence 90068 from Patent EP1572962.
JD485113 - Sequence 466137 from Patent EP1572962.
JD536864 - Sequence 517888 from Patent EP1572962.
JD369713 - Sequence 350737 from Patent EP1572962.
JD117456 - Sequence 98480 from Patent EP1572962.
JD532339 - Sequence 513363 from Patent EP1572962.
JD070922 - Sequence 51946 from Patent EP1572962.
JD193849 - Sequence 174873 from Patent EP1572962.
JD408231 - Sequence 389255 from Patent EP1572962.
JD040183 - Sequence 21207 from Patent EP1572962.
JD343532 - Sequence 324556 from Patent EP1572962.
JD127664 - Sequence 108688 from Patent EP1572962.
JD127098 - Sequence 108122 from Patent EP1572962.
JD070837 - Sequence 51861 from Patent EP1572962.
JD551157 - Sequence 532181 from Patent EP1572962.
JD566123 - Sequence 547147 from Patent EP1572962.
JD095339 - Sequence 76363 from Patent EP1572962.
JD339376 - Sequence 320400 from Patent EP1572962.
JD517073 - Sequence 498097 from Patent EP1572962.
JD171787 - Sequence 152811 from Patent EP1572962.
JD489852 - Sequence 470876 from Patent EP1572962.
JD548364 - Sequence 529388 from Patent EP1572962.
JD251878 - Sequence 232902 from Patent EP1572962.
JD231190 - Sequence 212214 from Patent EP1572962.
JD500782 - Sequence 481806 from Patent EP1572962.
JD136492 - Sequence 117516 from Patent EP1572962.
JD333809 - Sequence 314833 from Patent EP1572962.
JD454763 - Sequence 435787 from Patent EP1572962.
JD525057 - Sequence 506081 from Patent EP1572962.
JD250897 - Sequence 231921 from Patent EP1572962.
JD520838 - Sequence 501862 from Patent EP1572962.
JD279487 - Sequence 260511 from Patent EP1572962.
JD076893 - Sequence 57917 from Patent EP1572962.
JD469869 - Sequence 450893 from Patent EP1572962.
JD051121 - Sequence 32145 from Patent EP1572962.
JD566948 - Sequence 547972 from Patent EP1572962.
JD062038 - Sequence 43062 from Patent EP1572962.
JD546956 - Sequence 527980 from Patent EP1572962.
JD482401 - Sequence 463425 from Patent EP1572962.
JD255292 - Sequence 236316 from Patent EP1572962.
JD232320 - Sequence 213344 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000375759.1, ENST00000375759.2, ENST00000375759.3, ENST00000375759.4, ENST00000375759.5, ENST00000375759.6, ENST00000375759.7, KIAA0929, MINT, MINT_HUMAN, NM_015001, Q96T58, Q9H9A8, Q9NWH5, Q9UQ01, Q9Y556, SHARP, uc318mmm.1, uc318mmm.2
UCSC ID: ENST00000375759.8_4
RefSeq Accession: NM_015001.3
Protein: Q96T58 (aka MINT_HUMAN)

-  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.