Human Gene BBS9 (ENST00000242067.11_7) from GENCODE V47lift37
  Description: Bardet-Biedl syndrome 9, transcript variant 2 (from RefSeq NM_198428.3)
Gencode Transcript: ENST00000242067.11_7
Gencode Gene: ENSG00000122507.21_16
Transcript (Including UTRs)
   Position: hg19 chr7:33,169,176-33,645,681 Size: 476,506 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr7:33,185,865-33,644,838 Size: 458,974 Coding Exon Count: 22 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:33,169,176-33,645,681)mRNA (may differ from genome)Protein (887 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTHB1_HUMAN
DESCRIPTION: RecName: Full=Protein PTHB1; AltName: Full=Bardet-Biedl syndrome 9 protein; AltName: Full=Parathyroid hormone-responsive B1 gene protein;
FUNCTION: The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane.
SUBUNIT: Part of BBSome complex, that contains BBS1, BBS2, BBS4, BBS5, BBS7, BBS8, BBS9 and BBIP10. The BBSome complex binds to PCM1 and tubulin.
INTERACTION: Q8NFJ9:BBS1; NbExp=6; IntAct=EBI-2826852, EBI-1805484; Q8TAM1:BBS10; NbExp=2; IntAct=EBI-2826852, EBI-6128013; Q6ZW61:BBS12; NbExp=2; IntAct=EBI-2826852, EBI-6128352; Q9BXC9:BBS2; NbExp=9; IntAct=EBI-2826852, EBI-748297; Q8N3I7:BBS5; NbExp=3; IntAct=EBI-2826852, EBI-2892592; Q9NQ48:LZTFL1; NbExp=6; IntAct=EBI-2826852, EBI-2824799; Q8TAM2:TTC8; NbExp=2; IntAct=EBI-2826852, EBI-2892638;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome. Cell projection, cilium membrane. Cytoplasm. Note=Localizes to nonmembranous centriolar satellites in the cytoplasm.
TISSUE SPECIFICITY: Widely expressed. Expressed in adult heart, skeletal muscle, lung, liver, kidney, placenta and brain, and in fetal kidney, lung, liver and brain.
INDUCTION: Down-regulated by parathyroid hormone.
DISEASE: A chromosomal aberration involving PTHB1 is found in Wilms tumor 5 (WT5) [MIM:601583]. Translocation t(1;7)(q42;p15) with OBSCN.
DISEASE: Defects in BBS9 are a cause of Bardet-Biedl syndrome type 9 (BBS9) [MIM:209900]. Bardet-Biedl syndrome (BBS) is a genetically heterogeneous, autosomal recessive disorder characterized by usually severe pigmentary retinopathy, early onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation.
SEQUENCE CAUTION: Sequence=AAD25980.1; Type=Miscellaneous discrepancy; Note=Chimera; Sequence=AAD25981.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/BBS9";

-  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: BBS9
Diseases sorted by gene-association score: bardet-biedl syndrome 9* (1263), bardet-biedl syndrome* (311), bardet-biedl syndrome 11* (295), bardet-biedl syndrome 12* (283), bardet-biedl syndrome 10* (283), bardet-biedl syndrome 2* (231), bardet-biedl syndrome 1* (126), bbs9-related bardet-biedl syndrome* (100), bardet-biedl syndrome 3 (11), bardet-biedl syndrome 17 (7), bardet-biedl syndrome 14 (7)
* = 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: 7.96 RPKM in Pituitary
Total median expression: 148.55 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 -189.60489-0.388 Picture PostScript Text
3' UTR -195.10843-0.231 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
IPR026511 - PTHB1

Pfam Domains:
PF14727 - PTHB1 N-terminus
PF14728 - PTHB1 C-terminus

SCOP Domains:
50978 - WD40 repeat-like

ModBase Predicted Comparative 3D Structure on Q3SYG4
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:0003674 molecular_function
GO:0005515 protein binding

Biological Process:
GO:0007601 visual perception
GO:0015031 protein transport
GO:0030030 cell projection organization
GO:0045444 fat cell differentiation
GO:0050896 response to stimulus
GO:0060271 cilium assembly
GO:0061512 protein localization to cilium

Cellular Component:
GO:0000242 pericentriolar material
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0016020 membrane
GO:0034451 centriolar satellite
GO:0034464 BBSome
GO:0035869 ciliary transition zone
GO:0042995 cell projection
GO:0060170 ciliary membrane


-  Descriptions from all associated GenBank mRNAs
  LF384532 - JP 2014500723-A/192035: Polycomb-Associated Non-Coding RNAs.
BC003117 - Homo sapiens mRNA similar to PTH-responsive osteosarcoma B1 protein (cDNA clone IMAGE:3503650).
AK057660 - Homo sapiens cDNA FLJ33098 fis, clone TRACH2000780, highly similar to Parathyroid hormone-responsiveB1 gene protein.
BX647385 - Homo sapiens mRNA; cDNA DKFZp686A12144 (from clone DKFZp686A12144).
AK314627 - Homo sapiens cDNA, FLJ95469.
BC103831 - Homo sapiens Bardet-Biedl syndrome 9, mRNA (cDNA clone MGC:118917 IMAGE:40001794), complete cds.
AF095771 - Homo sapiens PTH-responsive osteosarcoma B1 protein (B1) mRNA, complete cds.
U85995 - Human clone IMAGE:22181 unknown protein mRNA, partial cds.
U87408 - Human clone IMAGE:74593 unknown protein mRNA, partial cds.
AK091361 - Homo sapiens cDNA FLJ34042 fis, clone FCBBF2006418, highly similar to Parathyroid hormone-responsive B1 gene protein.
U85994 - Human clone IMAGE:30008 unknown protein mRNA, partial cds.
AF095770 - Homo sapiens PTH-responsive osteosarcoma D1 protein (D1) mRNA, partial cds.
MA620109 - JP 2018138019-A/192035: Polycomb-Associated Non-Coding RNAs.
BC032715 - Homo sapiens Bardet-Biedl syndrome 9, mRNA (cDNA clone IMAGE:5519851), complete cds.
CU689500 - Synthetic construct Homo sapiens gateway clone IMAGE:100016690 5' read BBS9 mRNA.
KJ906120 - Synthetic construct Homo sapiens clone ccsbBroadEn_15790 BBS9 gene, encodes complete protein.
AK297436 - Homo sapiens cDNA FLJ53605 complete cds, highly similar to Parathyroid hormone-responsive B1 gene protein.
DQ584906 - Homo sapiens piRNA piR-52018, complete sequence.
JD072762 - Sequence 53786 from Patent EP1572962.
JD176040 - Sequence 157064 from Patent EP1572962.
AF095769 - Homo sapiens PTH-responsive osteosarcoma mRNA, partial 3'UTR.
JD097990 - Sequence 79014 from Patent EP1572962.
JD048545 - Sequence 29569 from Patent EP1572962.
JD465078 - Sequence 446102 from Patent EP1572962.
JD241008 - Sequence 222032 from Patent EP1572962.
JD242544 - Sequence 223568 from Patent EP1572962.
JD224326 - Sequence 205350 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q3SYG4 (Reactome details) participates in the following event(s):

R-HSA-5624125 Formation of the BBSome
R-HSA-5617815 BBSome binds RAB3IP
R-HSA-5624126 ARL6:GTP and the BBSome bind ciliary cargo
R-HSA-5624129 LZTFL1 binds the BBSome and prevents its traffic to the cilium
R-HSA-5620922 BBSome-mediated cargo-targeting to cilium
R-HSA-5620920 Cargo trafficking to the periciliary membrane
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: E9PDC9, ENST00000242067.1, ENST00000242067.10, ENST00000242067.2, ENST00000242067.3, ENST00000242067.4, ENST00000242067.5, ENST00000242067.6, ENST00000242067.7, ENST00000242067.8, ENST00000242067.9, NM_198428, P78514, PTHB1, PTHB1_HUMAN, Q3SYG4, Q7KYS6, Q7KYS7, Q8N570, Q99844, Q99854, Q9Y699, Q9Y6A0, uc317ejk.1, uc317ejk.2
UCSC ID: ENST00000242067.11_7
RefSeq Accession: NM_198428.3
Protein: Q3SYG4 (aka PTHB1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene BBS9:
bbs (Bardet-Biedl Syndrome Overview)

-  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.