Human Gene NHERF2 (ENST00000424542.7_6) from GENCODE V48lift37
  Description: NHERF family PDZ scaffold protein 2, transcript variant 1 (from RefSeq NM_001130012.3)
Gencode Transcript: ENST00000424542.7_6
Gencode Gene: ENSG00000065054.14_10
Transcript (Including UTRs)
   Position: hg19 chr16:2,076,903-2,089,027 Size: 12,125 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr16:2,077,007-2,087,985 Size: 10,979 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2025-04-10 15:10:12

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:2,076,903-2,089,027)mRNA (may differ from genome)Protein (337 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
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-  Comments and Description Text from UniProtKB
  ID: NHRF2_HUMAN
DESCRIPTION: RecName: Full=Na(+)/H(+) exchange regulatory cofactor NHE-RF2; Short=NHERF-2; AltName: Full=NHE3 kinase A regulatory protein E3KARP; AltName: Full=SRY-interacting protein 1; Short=SIP-1; AltName: Full=Sodium-hydrogen exchanger regulatory factor 2; AltName: Full=Solute carrier family 9 isoform A3 regulatory factor 2; AltName: Full=Tyrosine kinase activator protein 1; Short=TKA-1;
FUNCTION: Scaffold protein that connects plasma membrane proteins with members of the ezrin/moesin/radixin family and thereby helps to link them to the actin cytoskeleton and to regulate their surface expression. Necessary for cAMP-mediated phosphorylation and inhibition of SLC9A3. May also act as scaffold protein in the nucleus.
SUBUNIT: Homodimer, and heterodimer with SLC9A3R1. Binds PDZK1. Found in a complex with EZR, PODXL and SLC9A3R2 (By similarity). Interacts (via the PDZ domains) with PODXL (via the C-terminal PDZ-binding motif DTHL); interaction is detected in glomerular epithelium cells (By similarity). Binds ADRB2, SLC9A3, P2RY1, P2YR2, SRY, RDX and LPAR2. Interacts with MCC and PODXL. Interacts with SGK1 and KCNJ1/ROMK1.
INTERACTION: P13569:CFTR; NbExp=4; IntAct=EBI-1149760, EBI-349854; Q9HBW0:LPAR2; NbExp=2; IntAct=EBI-1149760, EBI-765995;
SUBCELLULAR LOCATION: Endomembrane system; Peripheral membrane protein. Nucleus. Apical cell membrane (By similarity). Note=Localizes with EZR and PODXL at the apical cell membrane of glomerular epithelium cells and the sides of the food processes (By similarity). Nuclear, in a punctate pattern.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Contains 2 PDZ (DHR) domains.
SEQUENCE CAUTION: Sequence=AAH14513.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAA90511.1; Type=Frameshift; Positions=309;

-  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: 86.33 RPKM in Lung
Total median expression: 1526.47 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 -54.40104-0.523 Picture PostScript Text
3' UTR -433.101042-0.416 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
IPR015098 - EBP50_C-term
IPR017300 - NaH_exchngr_reg_CF_NHE-RF
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain
PF09007 - EBP50, C-terminal
PF13180 - PDZ domain
PF17820 - PDZ domain

SCOP Domains:
50156 - PDZ domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2D11 - X-ray 2HE4 - X-ray MuPIT 2OCS - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15599
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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 Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0008022 protein C-terminus binding
GO:0019902 phosphatase binding
GO:0032947 protein complex scaffold
GO:0045296 cadherin binding

Biological Process:
GO:0065003 macromolecular complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ892753 - Synthetic construct Homo sapiens clone ccsbBroadEn_02147 SLC9A3R2 gene, encodes complete protein.
KJ898006 - Synthetic construct Homo sapiens clone ccsbBroadEn_07400 SLC9A3R2 gene, encodes complete protein.
BC106001 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2, mRNA (cDNA clone MGC:104639 IMAGE:5296143), complete cds.
BC014513 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2, mRNA (cDNA clone IMAGE:2958186), partial cds.
BC069014 - Homo sapiens solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2, mRNA (cDNA clone IMAGE:5431539), partial cds.
Z50150 - H.sapiens mRNA for tyrosine kinase activator protein 1 (TKA-1).
U82108 - Human SIP-1 mRNA, complete cds.
AF004900 - Homo sapiens NHE3 kinase A regulatory protein E3KARP mRNA, complete cds.
AF035771 - Homo sapiens Na+/H+ exchanger regulatory factor 2 (NHERF-2) mRNA, complete cds.
JD387462 - Sequence 368486 from Patent EP1572962.
JD104557 - Sequence 85581 from Patent EP1572962.
JD443162 - Sequence 424186 from Patent EP1572962.
JD260990 - Sequence 242014 from Patent EP1572962.
JD036563 - Sequence 17587 from Patent EP1572962.
JD332534 - Sequence 313558 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DU84, D3DU85, ENST00000424542.1, ENST00000424542.2, ENST00000424542.3, ENST00000424542.4, ENST00000424542.5, ENST00000424542.6, H3BSV6, NHERF2 , NHRF2_HUMAN, NM_001130012, O00272, O00556, Q15599, Q3KQY7, SLC9A3R2, uc319tus.1, uc319tus.2
UCSC ID: ENST00000424542.7_6
RefSeq Accession: NM_001130012.3
Protein: Q15599 (aka NHRF2_HUMAN or NHR2_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.