Human Gene TBC1D9B (uc003mlg.3)
  Description: Homo sapiens TBC1 domain family, member 9B (with GRAM domain) (TBC1D9B), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:179,289,071-179,298,805 Size: 9,735 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr5:179,290,448-179,298,473 Size: 8,026 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:179,289,071-179,298,805)mRNA (may differ from genome)Protein (409 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  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


-  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: 41.05 RPKM in Brain - Cerebellum
Total median expression: 1203.98 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 -50.00143-0.350 Picture PostScript Text
3' UTR -516.831377-0.375 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
IPR011992 - EF-hand-like_dom
IPR018249 - EF_HAND_2

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on G3V133
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding


-  Descriptions from all associated GenBank mRNAs
  AB014576 - Homo sapiens KIAA0676 mRNA for KIAA0676 protein.
BC129994 - Homo sapiens TBC1 domain family, member 9B (with GRAM domain), mRNA (cDNA clone MGC:157757 IMAGE:40129194), complete cds.
AB449893 - Homo sapiens TBC1D9B mRNA for TBC1 domain family, member 9B, complete cds.
AB463306 - Synthetic construct DNA, clone: pF1KA0676, Homo sapiens TBC1D9B gene for TBC1 domain family, member 9B, without stop codon, in Flexi system.
AK026096 - Homo sapiens cDNA: FLJ22443 fis, clone HRC09391.
BC000701 - Homo sapiens TBC1 domain family, member 9B (with GRAM domain), mRNA (cDNA clone IMAGE:3347537), complete cds.
BC008919 - Homo sapiens TBC1 domain family, member 9B (with GRAM domain), mRNA (cDNA clone IMAGE:3627916), complete cds.
BC080659 - Homo sapiens TBC1 domain family, member 9B (with GRAM domain), mRNA (cDNA clone IMAGE:6160217), partial cds.
BC110400 - Homo sapiens cDNA clone IMAGE:5557148.
AK001473 - Homo sapiens cDNA FLJ10611 fis, clone NT2RP2005315, highly similar to Homo sapiens mRNA for KIAA0676 protein.
AK001196 - Homo sapiens cDNA FLJ10334 fis, clone NT2RM2000649, highly similar to Homo sapiens mRNA for KIAA0676 protein.
BX641107 - Homo sapiens mRNA; cDNA DKFZp686O07131 (from clone DKFZp686O07131).
JD566624 - Sequence 547648 from Patent EP1572962.
JD124606 - Sequence 105630 from Patent EP1572962.
JD484204 - Sequence 465228 from Patent EP1572962.
JD115292 - Sequence 96316 from Patent EP1572962.
JD162592 - Sequence 143616 from Patent EP1572962.
JD260972 - Sequence 241996 from Patent EP1572962.
JD311548 - Sequence 292572 from Patent EP1572962.
JD207178 - Sequence 188202 from Patent EP1572962.
JD102490 - Sequence 83514 from Patent EP1572962.
JD226323 - Sequence 207347 from Patent EP1572962.
JD460125 - Sequence 441149 from Patent EP1572962.
JD552129 - Sequence 533153 from Patent EP1572962.
JD429522 - Sequence 410546 from Patent EP1572962.
BC031697 - Homo sapiens TBC1 domain family, member 9B (with GRAM domain), mRNA (cDNA clone IMAGE:4745422), with apparent retained intron.
AK123874 - Homo sapiens cDNA FLJ41880 fis, clone OCBBF2021020, weakly similar to Homo sapiens mRNA for vascular Rab-GAP/TBC-containing protein.
AK074791 - Homo sapiens cDNA FLJ90310 fis, clone NT2RP2001200, highly similar to Homo sapiens mRNA for KIAA0676 protein.
JD277778 - Sequence 258802 from Patent EP1572962.
JD417183 - Sequence 398207 from Patent EP1572962.
JD487331 - Sequence 468355 from Patent EP1572962.
JD243879 - Sequence 224903 from Patent EP1572962.
JD396828 - Sequence 377852 from Patent EP1572962.
JD097886 - Sequence 78910 from Patent EP1572962.
JD133320 - Sequence 114344 from Patent EP1572962.
JD399197 - Sequence 380221 from Patent EP1572962.
JD427255 - Sequence 408279 from Patent EP1572962.
JD527027 - Sequence 508051 from Patent EP1572962.
JD201170 - Sequence 182194 from Patent EP1572962.
JD193816 - Sequence 174840 from Patent EP1572962.
JD546240 - Sequence 527264 from Patent EP1572962.
JD045207 - Sequence 26231 from Patent EP1572962.
JD281560 - Sequence 262584 from Patent EP1572962.
JD418385 - Sequence 399409 from Patent EP1572962.
JD255306 - Sequence 236330 from Patent EP1572962.
JD191485 - Sequence 172509 from Patent EP1572962.
JD399862 - Sequence 380886 from Patent EP1572962.
JD541486 - Sequence 522510 from Patent EP1572962.
JD105509 - Sequence 86533 from Patent EP1572962.
AK223509 - Homo sapiens mRNA for KIAA0676 protein (Fragment) variant, clone: FCC121H06.
KJ902274 - Synthetic construct Homo sapiens clone ccsbBroadEn_11668 TBC1D9B gene, encodes complete protein.
JF432540 - Synthetic construct Homo sapiens clone IMAGE:100073763 TBC1 domain family, member 9B (with GRAM domain) (TBC1D9B) gene, encodes complete protein.
KJ906078 - Synthetic construct Homo sapiens clone ccsbBroadEn_15748 TBC1D9B gene, encodes complete protein.
AK304757 - Homo sapiens cDNA FLJ59011 complete cds, moderately similar to TBC1 domain family member 8.
AK127158 - Homo sapiens cDNA FLJ45221 fis, clone BRCAN2019907.
JD282553 - Sequence 263577 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC000701, G3V133, G3V133_HUMAN, hCG_15288, KIAA0676, NM_015043, NP_055858
UCSC ID: uc003mlg.3
RefSeq Accession: NM_015043
Protein: G3V133

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC000701.2
exon count: 8CDS single in 3' UTR: no RNA size: 2785
ORF size: 1230CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 2660.00frame shift in genome: no % Coverage: 98.74
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.