Human Gene EPDR1 (ENST00000199448.9_7) from GENCODE V47lift37
  Description: ependymin related 1, transcript variant 1 (from RefSeq NM_017549.5)
Gencode Transcript: ENST00000199448.9_7
Gencode Gene: ENSG00000086289.13_12
Transcript (Including UTRs)
   Position: hg19 chr7:37,960,242-37,991,538 Size: 31,297 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr7:37,960,542-37,989,998 Size: 29,457 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:37,960,242-37,991,538)mRNA (may differ from genome)Protein (224 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EPDR1_HUMAN
DESCRIPTION: RecName: Full=Mammalian ependymin-related protein 1; Short=MERP-1; AltName: Full=Upregulated in colorectal cancer gene 1 protein; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted.
SIMILARITY: Belongs to the ependymin family.
SEQUENCE CAUTION: Sequence=AAH00686.2; Type=Erroneous initiation; Sequence=CAB60269.1; 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


-  MalaCards Disease Associations
  MalaCards Gene Search: EPDR1
Diseases sorted by gene-association score: colorectal cancer (1)

-  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: 55.70 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 764.57 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -126.90300-0.423 Picture PostScript Text
3' UTR -409.501540-0.266 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
IPR001299 - Ependymin
IPR018224 - Ependymin_CS

Pfam Domains:
PF00811 - Ependymin

ModBase Predicted Comparative 3D Structure on Q9UM22
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:0005509 calcium ion binding

Biological Process:
GO:0007160 cell-matrix adhesion

Cellular Component:
GO:0005576 extracellular region
GO:0005764 lysosome


-  Descriptions from all associated GenBank mRNAs
  AY027862 - Homo sapiens mammalian ependymin related protein 1 (MERP1) mRNA, complete cds.
BC018299 - Homo sapiens ependymin related protein 1 (zebrafish), mRNA (cDNA clone MGC:17297 IMAGE:3461888), complete cds.
BC000686 - Homo sapiens ependymin related protein 1 (zebrafish), mRNA (cDNA clone IMAGE:3347737), partial cds.
AK290885 - Homo sapiens cDNA FLJ78572 complete cds, highly similar to Homo sapiens ependymin related protein-1 (MERP1) gene.
KJ902679 - Synthetic construct Homo sapiens clone ccsbBroadEn_12073 EPDR1 gene, encodes complete protein.
DQ914439 - Homo sapiens mammalian ependymin protein 1a (EPDR1) mRNA, complete cds, alternatively spliced.
JD192911 - Sequence 173935 from Patent EP1572962.
JD230680 - Sequence 211704 from Patent EP1572962.
JD426351 - Sequence 407375 from Patent EP1572962.
AJ250475 - Homo sapiens mRNA for UCC1 protein (UCC1 gene).
AK309180 - Homo sapiens cDNA, FLJ99221.
JD460532 - Sequence 441556 from Patent EP1572962.
JD436201 - Sequence 417225 from Patent EP1572962.
JD043378 - Sequence 24402 from Patent EP1572962.
JD452372 - Sequence 433396 from Patent EP1572962.
JD270084 - Sequence 251108 from Patent EP1572962.
JD336129 - Sequence 317153 from Patent EP1572962.
JD192217 - Sequence 173241 from Patent EP1572962.
JD116043 - Sequence 97067 from Patent EP1572962.
JD393641 - Sequence 374665 from Patent EP1572962.
JD554070 - Sequence 535094 from Patent EP1572962.
JD322217 - Sequence 303241 from Patent EP1572962.
JD132899 - Sequence 113923 from Patent EP1572962.
JD132900 - Sequence 113924 from Patent EP1572962.
JD493784 - Sequence 474808 from Patent EP1572962.
JD512389 - Sequence 493413 from Patent EP1572962.
JD561107 - Sequence 542131 from Patent EP1572962.
JD510356 - Sequence 491380 from Patent EP1572962.
JD081385 - Sequence 62409 from Patent EP1572962.
JD048955 - Sequence 29979 from Patent EP1572962.
AX229887 - Sequence 13 from Patent WO0162959.
JD552519 - Sequence 533543 from Patent EP1572962.
JD206401 - Sequence 187425 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4C0, C9JYS3, ENST00000199448.1, ENST00000199448.2, ENST00000199448.3, ENST00000199448.4, ENST00000199448.5, ENST00000199448.6, ENST00000199448.7, ENST00000199448.8, EPDR1_HUMAN, MERP1, NM_017549, Q06BL0, Q99M77, Q9UM22, uc317chl.1, uc317chl.2, UCC1
UCSC ID: ENST00000199448.9_7
RefSeq Accession: NM_017549.5
Protein: Q9UM22 (aka EPDR1_HUMAN)

-  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.