Human Gene AVL9 (uc010kwj.1)
  Description: Homo sapiens AVL9 homolog (S. cerevisiase) (AVL9), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:32,584,306-32,623,779 Size: 39,474 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr7:32,591,856-32,623,658 Size: 31,803 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:32,584,306-32,623,779)mRNA (may differ from genome)Protein (478 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedUniProtKB

-  Comments and Description Text from UniProtKB
  ID: H7C0I1_HUMAN
DESCRIPTION: SubName: Full=Late secretory pathway protein AVL9 homolog; Flags: Fragment;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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

+  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: 5.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 156.66 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.55263-0.223 Picture PostScript Text
3' UTR -28.00121-0.231 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
IPR018307 - Secretory_pathway_prot_Avl9

Pfam Domains:
PF08616 - Stabilization of polarity axis
PF09794 - Transport protein Avl9

ModBase Predicted Comparative 3D Structure on H7C0I1
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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC027724 - Homo sapiens AVL9 homolog (S. cerevisiase), mRNA (cDNA clone MGC:23182 IMAGE:4811237), complete cds.
AK090619 - Homo sapiens cDNA FLJ33300 fis, clone BNGH42002168.
AX746537 - Sequence 62 from Patent EP1308459.
CU693288 - Synthetic construct Homo sapiens gateway clone IMAGE:100022015 5' read KIAA0241 mRNA.
D87682 - Homo sapiens mRNA for KIAA0241 gene, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: D87682, H7C0I1, H7C0I1_HUMAN
UCSC ID: uc010kwj.1
RefSeq Accession: NM_015060
Protein: H7C0I1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: D87682.1
exon count: 12CDS single in 3' UTR: no RNA size: 6371
ORF size: 1437CDS single in intron: no Alignment % ID: 99.86
txCdsPredict score: 2825.00frame shift in genome: no % Coverage: 28.58
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.