Human Gene SEPT9 (uc002jtt.4) Description and Page Index
  Description: Homo sapiens septin 9 (SEPT9), transcript variant 5, mRNA.
RefSeq Summary (NM_001113492): This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009].
Transcript (Including UTRs)
   Position: hg19 chr17:75,283,973-75,496,678 Size: 212,706 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr17:75,398,557-75,494,740 Size: 96,184 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr17:75,283,973-75,496,678)mRNA (may differ from genome)Protein (422 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Septin-9; AltName: Full=MLL septin-like fusion protein MSF-A; Short=MLL septin-like fusion protein; AltName: Full=Ovarian/Breast septin; Short=Ov/Br septin; AltName: Full=Septin D1;
FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). May play a role in the internalization of 2 intracellular microbial pathogens, Listeria monocytogenes and Shigella flexneri.
SUBUNIT: Septins polymerize into heterooligomeric protein complexes that form filaments, and associate with cellular membranes, actin filaments, and microtubules. GTPase activity is required for filament formation. Interacts with SEPT2, SEPT6, SEPT7, SEPT11 and SEPT14. Interacts with RTKN and ARHGEF18. In a mesenchymal cell line, Rho/RTKN signals cause disruption of wild- type septin filaments, but not of those containing isoform 2 variants HNA Trp-106 and Phe-111. In a mesenchymal cell line, isoform 2 variants HNA Trp-106 and Phe-111, but not wild type, form filaments with SEPT4.
INTERACTION: Q16665:HIF1A; NbExp=4; IntAct=EBI-851558, EBI-447269; Q6ZU15:SEPT14; NbExp=3; IntAct=EBI-851569, EBI-2009297;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Note=In an epithelial cell line, concentrates at cell-cell contact areas. After TGF-beta1 treatment and induction of epithelial to mesenchymal transition, colocalizes partly with actin stress fibers. During bacterial infection, displays a collar shape structure next to actin at the pole of invading bacteria.
TISSUE SPECIFICITY: Widely expressed. Isoforms are differentially expressed in testes, kidney, liver heart, spleen, brain, peripheral blood leukocytes, skeletal muscle and kidney. Specific isoforms appear to demonstrate tissue specificity. Isoform 5 is the most highly expressed in fetal tissue. Isoform 1 is detected in all tissues except the brain and thymus, while isoform 2, isoform 3, and isoform 4 are detected at low levels in approximately half of the fetal tissues.
DISEASE: Note=A chromosomal aberration involving SEPT9/MSF is found in therapy-related acute myeloid leukemia (t-AML). Translocation t(11;17)(q23;q25) with MLL.
DISEASE: Defects in SEPT9 are a cause of hereditary neuralgic amyotrophy (HNA) [MIM:162100]; also known as neuritis with brachial predilection (NAPB) or hereditary brachial plexus neuropathy or hereditary neuralgic amyotrophy with predilection for brachial plexus. HNA is an autosomal dominant form of recurrent focal neuropathy characterized clinically by acute, recurrent episodes of brachial plexus neuropathy with muscle weakness and atrophy preceded by severe pain in the affected arm. HNA is triggered by environmental factors such as infection or parturition.
SIMILARITY: Belongs to the septin family.
SEQUENCE CAUTION: Sequence=BAB14057.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";
WEB RESOURCE: Name=GeneReviews; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SEPT9
CDC HuGE Published Literature: SEPT9
Positive Disease Associations: Body Fat Distribution , Body Height , Body Mass Index , Lipoproteins , Tunica Media
Related Studies:
  1. Body Fat Distribution
    , , . [PubMed 0]
  2. Body Height
    , , . [PubMed 0]
  3. Body Mass Index
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SEPT9
Diseases sorted by gene-association score: amyotrophy, hereditary neuralgic* (1325), brachial plexus neuropathy (37), amyotrophic neuralgia (30), brachial plexus neuritis (16), cri-du-chat syndrome (9)
* = 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: 60.95 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 927.49 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 -363.20793-0.458 Picture PostScript Text
3' UTR -825.201938-0.426 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
IPR000038 - Cell_div_GTP-bd

Pfam Domains:
PF00735 - Septin
PF01926 - 50S ribosome-binding GTPase

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9UHD8
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:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0045296 cadherin binding

Biological Process:
GO:0007049 cell cycle
GO:0051291 protein heterooligomerization
GO:0051301 cell division
GO:1902857 positive regulation of non-motile cilium assembly

Cellular Component:
GO:0001725 stress fiber
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005930 axoneme
GO:0015629 actin cytoskeleton
GO:0031105 septin complex
GO:0048471 perinuclear region of cytoplasm
GO:0097730 non-motile cilium

-  Descriptions from all associated GenBank mRNAs
  EU427520 - Homo sapiens septin 9/TNRC6C fusion mRNA, partial sequence.
AK027069 - Homo sapiens cDNA: FLJ23416 fis, clone HEP20790.
AF189712 - Homo sapiens MLL septin-like fusion protein MSF-B mRNA, complete cds, alternatively spliced.
AF189713 - Homo sapiens MLL septin-like fusion protein MSF-A mRNA, complete cds, alternatively spliced.
AK300270 - Homo sapiens cDNA FLJ54882 complete cds, highly similar to Septin-9.
AK300268 - Homo sapiens cDNA FLJ55422 complete cds, highly similar to Septin-9.
BC054004 - Homo sapiens septin 9, mRNA (cDNA clone MGC:61648 IMAGE:6146448), complete cds.
AK290368 - Homo sapiens cDNA FLJ75490 complete cds, highly similar to Homo sapiens septin 9, mRNA.
AJ312321 - Homo sapiens mRNA for OVARIAN/Breast septin alpha (Ov/Br septin gene).
AF123052 - Homo sapiens MLL septin-like fusion protein (MSF) mRNA, complete cds.
AF142408 - Homo sapiens cell division control protein septin D1 mRNA, complete cds.
BC021192 - Homo sapiens septin 9, mRNA (cDNA clone MGC:1292 IMAGE:3346534), complete cds.
CU676864 - Synthetic construct Homo sapiens gateway clone IMAGE:100018366 5' read SEPT9 mRNA.
KU178538 - Homo sapiens septin 9 isoform 3 (SEPT9) mRNA, partial cds, alternatively spliced.
KU178539 - Homo sapiens septin 9 isoform 1 (SEPT9) mRNA, partial cds.
DQ893792 - Synthetic construct Homo sapiens clone IMAGE:100008252; FLH164430.01L; RZPDo839G03161D septin 9 (SEPT9) gene, encodes complete protein.
KJ898291 - Synthetic construct Homo sapiens clone ccsbBroadEn_07685 SEPT9 gene, encodes complete protein.
BT007215 - Homo sapiens MLL septin-like fusion mRNA, complete cds.
DQ890623 - Synthetic construct clone IMAGE:100003253; FLH164434.01X; RZPDo839G03162D septin 9 (SEPT9) gene, encodes complete protein.
AJ312323 - Homo sapiens partial mRNA for OVARIAN/Breast septin epsilon (Ov/Br septin gene).
AJ312319 - Homo sapiens mRNA for OVARIAN/Breast septin gamma (Ov/Br septin gene).
AK304143 - Homo sapiens cDNA FLJ54900 complete cds, highly similar to Septin-9.
AB023208 - Homo sapiens KIAA0991 mRNA for KIAA0991 protein.
AJ312322 - Homo sapiens mRNA for OVARIAN/Breast septin beta (Ov/Br septin gene).
BC114550 - Homo sapiens septin 9, mRNA (cDNA clone IMAGE:40035301), partial cds.
AK303449 - Homo sapiens cDNA FLJ55268 complete cds, highly similar to Septin-9.
AJ312320 - Homo sapiens mRNA for OVARIAN/Breast septin delta (Ov/Br septin gene).
AK022493 - Homo sapiens cDNA FLJ12431 fis, clone MAMMA1003166, highly similar to Homo sapiens MLL septin-like fusion protein (MSF) mRNA.
AK299828 - Homo sapiens cDNA FLJ58686 complete cds, highly similar to Septin-9.
AK316473 - Homo sapiens cDNA, FLJ79372 complete cds, highly similar to Septin-9.
AK056495 - Homo sapiens cDNA FLJ31933 fis, clone NT2RP7006304, highly similar to Septin-9.
AL080131 - Homo sapiens mRNA; cDNA DKFZp434F243 (from clone DKFZp434F243).
BC128416 - Homo sapiens v-maf musculoaponeurotic fibrosarcoma oncogene homolog K (avian), mRNA (cDNA clone IMAGE:40117681), partial cds.
JD388625 - Sequence 369649 from Patent EP1572962.
JD118917 - Sequence 99941 from Patent EP1572962.
AF142569 - Homo sapiens hypothetical protein SBBI23 (SBBI23) mRNA, complete cds.
JD115932 - Sequence 96956 from Patent EP1572962.
JD472657 - Sequence 453681 from Patent EP1572962.
JD155988 - Sequence 137012 from Patent EP1572962.
JD534950 - Sequence 515974 from Patent EP1572962.
JD177597 - Sequence 158621 from Patent EP1572962.
JD475238 - Sequence 456262 from Patent EP1572962.
JD442238 - Sequence 423262 from Patent EP1572962.
JD076016 - Sequence 57040 from Patent EP1572962.
JD327015 - Sequence 308039 from Patent EP1572962.
JD368735 - Sequence 349759 from Patent EP1572962.
JD218239 - Sequence 199263 from Patent EP1572962.
JD547219 - Sequence 528243 from Patent EP1572962.
JD232369 - Sequence 213393 from Patent EP1572962.
BC064642 - Homo sapiens cDNA clone IMAGE:5772724, partial cds.
JD390902 - Sequence 371926 from Patent EP1572962.
JD271711 - Sequence 252735 from Patent EP1572962.
JD361404 - Sequence 342428 from Patent EP1572962.
JD187641 - Sequence 168665 from Patent EP1572962.
JD354475 - Sequence 335499 from Patent EP1572962.
JD211649 - Sequence 192673 from Patent EP1572962.
JD132553 - Sequence 113577 from Patent EP1572962.
JD267942 - Sequence 248966 from Patent EP1572962.
JD341084 - Sequence 322108 from Patent EP1572962.
BC018877 - Homo sapiens septin 9, mRNA (cDNA clone IMAGE:3620696).
JD180788 - Sequence 161812 from Patent EP1572962.
JD222585 - Sequence 203609 from Patent EP1572962.
JD343147 - Sequence 324171 from Patent EP1572962.
JD230159 - Sequence 211183 from Patent EP1572962.
JD181126 - Sequence 162150 from Patent EP1572962.
JD157414 - Sequence 138438 from Patent EP1572962.
JD209789 - Sequence 190813 from Patent EP1572962.
JD285027 - Sequence 266051 from Patent EP1572962.
JD354187 - Sequence 335211 from Patent EP1572962.
JD387320 - Sequence 368344 from Patent EP1572962.
JD189416 - Sequence 170440 from Patent EP1572962.
JD054907 - Sequence 35931 from Patent EP1572962.
JD413125 - Sequence 394149 from Patent EP1572962.
JD072471 - Sequence 53495 from Patent EP1572962.
JD138604 - Sequence 119628 from Patent EP1572962.
JD126749 - Sequence 107773 from Patent EP1572962.
JD145485 - Sequence 126509 from Patent EP1572962.
JD506831 - Sequence 487855 from Patent EP1572962.
JD218845 - Sequence 199869 from Patent EP1572962.
JD530154 - Sequence 511178 from Patent EP1572962.
JD289409 - Sequence 270433 from Patent EP1572962.
JD394064 - Sequence 375088 from Patent EP1572962.
JD516590 - Sequence 497614 from Patent EP1572962.
JD515559 - Sequence 496583 from Patent EP1572962.
JD260716 - Sequence 241740 from Patent EP1572962.
JD266928 - Sequence 247952 from Patent EP1572962.
JD293047 - Sequence 274071 from Patent EP1572962.
JD305225 - Sequence 286249 from Patent EP1572962.
JD477333 - Sequence 458357 from Patent EP1572962.
JD459792 - Sequence 440816 from Patent EP1572962.
JD498852 - Sequence 479876 from Patent EP1572962.
JD370814 - Sequence 351838 from Patent EP1572962.
JD549900 - Sequence 530924 from Patent EP1572962.
JD168048 - Sequence 149072 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2V3, B3KPM0, B4DTL9, B4E0N2, B4E274, B7Z654, KIAA0991, MSF, NM_001113492, NP_001106966, Q96QF3, Q96QF4, Q96QF5, Q9HA04, Q9UG40, Q9UHD8, Q9Y5W4, SEPT9_HUMAN
UCSC ID: uc002jtt.4
RefSeq Accession: NM_001113492
Protein: Q9UHD8 (aka SEPT9_HUMAN)
CCDS: CCDS45793.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001113492.1
exon count: 12CDS single in 3' UTR: no RNA size: 4012
ORF size: 1269CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 1593.00frame shift in genome: no % Coverage: 99.70
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.