Human Gene OCEL1 (uc002nfp.3)
  Description: Homo sapiens occludin/ELL domain containing 1 (OCEL1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:17,337,055-17,340,028 Size: 2,974 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr19:17,337,057-17,339,734 Size: 2,678 Coding Exon Count: 6 

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 (chr19:17,337,055-17,340,028)mRNA (may differ from genome)Protein (264 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: OCEL1_HUMAN
DESCRIPTION: RecName: Full=Occludin/ELL domain-containing protein 1;
SIMILARITY: Belongs to the ELL/occludin family.

-  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: 18.95 RPKM in Liver
Total median expression: 421.37 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
3' UTR -98.60294-0.335 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
IPR010844 - Occludin_RNApol2_elong_fac_ELL

Pfam Domains:
PF07303 - Occludin homology domain

ModBase Predicted Comparative 3D Structure on Q9H607
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
  BC029361 - Homo sapiens occludin/ELL domain containing 1, mRNA (cDNA clone MGC:32535 IMAGE:4064124), complete cds.
BC038945 - Homo sapiens occludin/ELL domain containing 1, mRNA (cDNA clone IMAGE:5200893), with apparent retained intron.
AK026362 - Homo sapiens cDNA: FLJ22709 fis, clone HSI13338.
CU688632 - Synthetic construct Homo sapiens gateway clone IMAGE:100022139 5' read OCEL1 mRNA.
HQ447782 - Synthetic construct Homo sapiens clone IMAGE:100071123; CCSB013178_01 occludin/ELL domain containing 1 (OCEL1) gene, encodes complete protein.
BC004121 - Homo sapiens occludin/ELL domain containing 1, mRNA (cDNA clone IMAGE:3927742), complete cds.
AF109191 - Homo sapiens FWP009 mRNA, complete cds.
JD390849 - Sequence 371873 from Patent EP1572962.
JD535222 - Sequence 516246 from Patent EP1572962.
JD353918 - Sequence 334942 from Patent EP1572962.
JD403070 - Sequence 384094 from Patent EP1572962.
JD378800 - Sequence 359824 from Patent EP1572962.
JD525953 - Sequence 506977 from Patent EP1572962.
JD414603 - Sequence 395627 from Patent EP1572962.
JD514566 - Sequence 495590 from Patent EP1572962.
JD044999 - Sequence 26023 from Patent EP1572962.
JD174998 - Sequence 156022 from Patent EP1572962.
JD225644 - Sequence 206668 from Patent EP1572962.
JD385939 - Sequence 366963 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_024578, NP_078854, OCEL1_HUMAN, Q9H607
UCSC ID: uc002nfp.3
RefSeq Accession: NM_024578
Protein: Q9H607 (aka OCEL1_HUMAN)
CCDS: CCDS12351.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024578.1
exon count: 6CDS single in 3' UTR: no RNA size: 1124
ORF size: 795CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 1690.00frame shift in genome: no % Coverage: 97.06
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.