Human Gene PDZRN4 (ENST00000402685.7_4) from GENCODE V47lift37
  Description: PDZ domain containing ring finger 4, transcript variant 1 (from RefSeq NM_001164595.2)
Gencode Transcript: ENST00000402685.7_4
Gencode Gene: ENSG00000165966.16_8
Transcript (Including UTRs)
   Position: hg19 chr12:41,582,122-41,968,547 Size: 386,426 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr12:41,582,258-41,967,692 Size: 385,435 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:41,582,122-41,968,547)mRNA (may differ from genome)Protein (1036 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PZRN4_HUMAN
DESCRIPTION: RecName: Full=PDZ domain-containing RING finger protein 4; AltName: Full=Ligand of Numb protein X 4; AltName: Full=SEMACAP3-like protein;
SIMILARITY: Contains 2 PDZ (DHR) domains.
SIMILARITY: Contains 1 RING-type zinc finger.

-  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: 16.49 RPKM in Colon - Sigmoid
Total median expression: 122.50 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 -59.40136-0.437 Picture PostScript Text
3' UTR -178.30855-0.209 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
IPR001478 - PDZ
IPR013323 - SIAH-type
IPR008974 - TRAF-like
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF00595 - PDZ domain
PF13180 - PDZ domain
PF13445 - RING-type zinc-finger
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF17820 - PDZ domain

SCOP Domains:
50156 - PDZ domain-like
49599 - TRAF domain-like
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q6ZMN7
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0046872 metal ion binding


-  Descriptions from all associated GenBank mRNAs
  AK294535 - Homo sapiens cDNA FLJ59319 complete cds, highly similar to PDZ domain-containing RING finger protein 4.
AK294431 - Homo sapiens cDNA FLJ52105 complete cds, highly similar to PDZ domain-containing RING finger protein 4.
AK131554 - Homo sapiens cDNA FLJ16796 fis, clone TBAES2008133, moderately similar to Mus musculus semaF cytoplasmic domain associated protein 3.
AK091096 - Homo sapiens cDNA FLJ33777 fis, clone BRSSN2000561, moderately similar to Mus musculus semaphorin cytoplasmic domain-associated protein 3A (Semcap3) mRNA.
AX746777 - Sequence 302 from Patent EP1308459.
BC093744 - Homo sapiens PDZ domain containing ring finger 4, mRNA (cDNA clone MGC:120779 IMAGE:7939589), complete cds.
BC093746 - Homo sapiens PDZ domain containing ring finger 4, mRNA (cDNA clone MGC:120781 IMAGE:7939591), complete cds.
KJ898752 - Synthetic construct Homo sapiens clone ccsbBroadEn_08146 PDZRN4 gene, encodes complete protein.
BX640695 - Homo sapiens mRNA; cDNA DKFZp779I162 (from clone DKFZp779I162).
BC040922 - Homo sapiens PDZ domain containing ring finger 4, mRNA (cDNA clone IMAGE:5767589), partial cds.
AK094690 - Homo sapiens cDNA FLJ37371 fis, clone BRAMY2024711, highly similar to PDZ domain-containing RING finger protein 4.
JD065001 - Sequence 46025 from Patent EP1572962.
AL133067 - Homo sapiens mRNA; cDNA DKFZp434B0417 (from clone DKFZp434B0417).
JD236961 - Sequence 217985 from Patent EP1572962.
JD299870 - Sequence 280894 from Patent EP1572962.
JD526688 - Sequence 507712 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000402685.1, ENST00000402685.2, ENST00000402685.3, ENST00000402685.4, ENST00000402685.5, ENST00000402685.6, LNX4, NM_001164595, PZRN4_HUMAN, Q52LY3, Q52LY4, Q6N052, Q6ZMN7, Q8IUU1, Q9NTP7, SEMCAP3L, uc319bxq.1, uc319bxq.2
UCSC ID: ENST00000402685.7_4
RefSeq Accession: NM_001164595.2
Protein: Q6ZMN7 (aka PZRN4_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.