Human Gene ODR4 (uc021pgj.1)
  Description: Homo sapiens chromosome 1 open reading frame 27 (ODR4), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:186,348,899-186,390,503 Size: 41,605 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr1:186,348,918-186,388,208 Size: 39,291 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene 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 (chr1:186,348,899-186,390,503)mRNA (may differ from genome)Protein (454 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
LynxMGIneXtProtOMIMPubMedTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ODR4_HUMAN
DESCRIPTION: RecName: Full=Protein odr-4 homolog; Short=hODR-4; AltName: Full=LAG1-interacting protein; AltName: Full=Transactivated by transforming growth factor beta protein 1;
FUNCTION: May play a role in the trafficking of a subset of G- protein coupled receptors (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the ODR-4 family.
SEQUENCE CAUTION: Sequence=BAB15356.1; Type=Erroneous initiation;

-  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


+  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: 11.18 RPKM in Prostate
Total median expression: 337.74 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 -0.2019-0.011 Picture PostScript Text
3' UTR -538.082295-0.234 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
IPR002085 - ADH_SF_Zn-type

Pfam Domains:
PF14778 - Olfactory receptor 4-like

ModBase Predicted Comparative 3D Structure on Q5SWX8
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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF205387 - JP 2014500723-A/12890: Polycomb-Associated Non-Coding RNAs.
AK298107 - Homo sapiens cDNA FLJ54926 complete cds.
AK000512 - Homo sapiens cDNA FLJ20505 fis, clone KAT09459.
AY854248 - Homo sapiens odorant response abnormal 4 protein mRNA, complete cds.
BC003397 - Homo sapiens chromosome 1 open reading frame 27, mRNA (cDNA clone MGC:4960 IMAGE:3448518), complete cds.
DQ323046 - Homo sapiens TTG1 mRNA, complete cds.
DQ529299 - Homo sapiens TTG1A mRNA, complete cds.
AK026086 - Homo sapiens cDNA: FLJ22433 fis, clone HRC09172.
KJ902726 - Synthetic construct Homo sapiens clone ccsbBroadEn_12120 C1orf27 gene, encodes complete protein.
AK000171 - Homo sapiens cDNA FLJ20164 fis, clone COL09448.
AF214011 - Homo sapiens putative LAG1-interacting protein mRNA, partial cds.
MA440964 - JP 2018138019-A/12890: Polycomb-Associated Non-Coding RNAs.
JD380822 - Sequence 361846 from Patent EP1572962.
CU678454 - Synthetic construct Homo sapiens gateway clone IMAGE:100019129 5' read C1orf27 mRNA.
LF319890 - JP 2014500723-A/127393: Polycomb-Associated Non-Coding RNAs.
LF319889 - JP 2014500723-A/127392: Polycomb-Associated Non-Coding RNAs.
MA555467 - JP 2018138019-A/127393: Polycomb-Associated Non-Coding RNAs.
MA555466 - JP 2018138019-A/127392: Polycomb-Associated Non-Coding RNAs.
JD502668 - Sequence 483692 from Patent EP1572962.
LF319888 - JP 2014500723-A/127391: Polycomb-Associated Non-Coding RNAs.
JD361608 - Sequence 342632 from Patent EP1572962.
JD085274 - Sequence 66298 from Patent EP1572962.
JD562544 - Sequence 543568 from Patent EP1572962.
JD454966 - Sequence 435990 from Patent EP1572962.
JD542601 - Sequence 523625 from Patent EP1572962.
JD238542 - Sequence 219566 from Patent EP1572962.
JD167290 - Sequence 148314 from Patent EP1572962.
JD180274 - Sequence 161298 from Patent EP1572962.
JD135179 - Sequence 116203 from Patent EP1572962.
JD560090 - Sequence 541114 from Patent EP1572962.
JD441395 - Sequence 422419 from Patent EP1572962.
JD319405 - Sequence 300429 from Patent EP1572962.
JD383924 - Sequence 364948 from Patent EP1572962.
LF319887 - JP 2014500723-A/127390: Polycomb-Associated Non-Coding RNAs.
LF319886 - JP 2014500723-A/127389: Polycomb-Associated Non-Coding RNAs.
MA555465 - JP 2018138019-A/127391: Polycomb-Associated Non-Coding RNAs.
MA555464 - JP 2018138019-A/127390: Polycomb-Associated Non-Coding RNAs.
MA555463 - JP 2018138019-A/127389: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DNY0, C1orf27, CCDS53448, E9PFR7, NM_017847, NP_060317, ODR4_HUMAN, Q19CC6, Q5SWX8, Q8WYB6, Q9BTS2, Q9H6A6, Q9NX06, TTG1, TTG1A
UCSC ID: uc021pgj.1
RefSeq Accession: NM_017847
Protein: Q5SWX8 (aka ODR4_HUMAN)
CCDS: CCDS53448.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: CCDS53448.1
exon count: 13CDS single in 3' UTR: no RNA size: 3679
ORF size: 1365CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2930.00frame shift in genome: no % Coverage: 100.00
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: 1
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.