Human Gene NDFIP1 (uc003lmi.4)
  Description: Homo sapiens Nedd4 family interacting protein 1 (NDFIP1), mRNA.
RefSeq Summary (NM_030571): The protein encoded by this gene belongs to a small group of evolutionarily conserved proteins with three transmembrane domains. It is a potential target for ubiquitination by the Nedd4 family of proteins. This protein is thought to be part of a family of integral Golgi membrane proteins. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr5:141,488,324-141,534,008 Size: 45,685 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr5:141,488,540-141,524,239 Size: 35,700 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:141,488,324-141,534,008)mRNA (may differ from genome)Protein (221 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NFIP1_HUMAN
DESCRIPTION: RecName: Full=NEDD4 family-interacting protein 1; AltName: Full=Breast cancer-associated protein SGA-1M; AltName: Full=NEDD4 WW domain-binding protein 5; AltName: Full=Putative MAPK-activating protein PM13; AltName: Full=Putative NF-kappa-B-activating protein 164; AltName: Full=Putative NFKB and MAPK-activating protein;
FUNCTION: Activates HECT domain-containing E3 ubiquitin-protein ligases, including NEDD4 and ITCH, and consequently modulates the stability of their targets. As a result, controls many cellular processes. Prevents chronic T-helper cells-mediated inflammation by activating ITCH and thus controlling JUNB degradation (By similarity). In cortical neurons, mediates the ubiquitination of SLC11A2/DMT1 by NEDD4L, leading to down-regulation of the divalent metal transporter and protection of the cells from cobalt and iron toxicity. Modulates EGFR signaling through multiple pathways. In particular, may regulate the ratio of AKT1-to-MAPK8 signaling in response to EGF, acting on AKT1 probably through PTEN destabilization and on MAPK8 through ITCH-dependent MAP2K4 inactivation. As a result, may control cell growth rate.
SUBUNIT: Forms heterodimers with NDFIP2. Interacts with several E3 ubiquitin-protein ligases, including NEDD4, NEDD4L and WWP2. Interacts with ITCH, U2SURP and WWP2 (By similarity). The interaction with NEDD4, NEDD4L and ITCH leads to relocalization of these proteins to exosomes and eventually to exosomal secretion. Interacts with SLC11A2/DMT1. Interacts with PTEN. May interact with phosphorylated EGFR.
SUBCELLULAR LOCATION: Endosome membrane; Multi-pass membrane protein. Golgi apparatus membrane (By similarity). Secreted. Note=Detected in exosomes and secreted via the exosomal pathway.
TISSUE SPECIFICITY: Widely expressed. Higher levels are detected in cerebellum, pituitary, thalamus, kidney, liver, testis, salivary glands and placenta. Also expressed in fetal brain, kidney and lung.
INDUCTION: Increased protein expression in neuronal cells in response to Co(2+) or Fe(2+) ions.
DOMAIN: The PY (WW-binding) motifs are required for E3 ubiquitin- protein ligase binding and activation and for ubiquitination.
PTM: Ubiquitinated by NEDD4 and ITCH; mono-, di- and polyubiquitinated forms are detected. Ubiquitination regulates its degradation.
PTM: Undergoes transient tyrosine phosphorylation following EGF stimulation, most probably by catalyzed by SRC. Phosphorylation SRC is enhanced in the presence of NDFIP2 which may act as a scaffold to recruit SRC to NDFIP1.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NDFIP1
CDC HuGE Published Literature: NDFIP1
Positive Disease Associations: Multiple Sclerosis , Testicular Neoplasms
Related Studies:
  1. Multiple Sclerosis
    Stephen Sawcer et al. Nature 2011, Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis., Nature. [PubMed 21833088]
  2. Testicular Neoplasms
    Elizabeth A Rapley et al. Nature genetics 2009, A genome-wide association study of testicular germ cell tumor., Nature genetics. [PubMed 19483681]
  3. Testicular Neoplasms
    Clare Turnbull et al. Nature genetics 2010, Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer., Nature genetics. [PubMed 20543847]
           more ... click here to view the complete list

-  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: 100.61 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1917.42 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 -88.80216-0.411 Picture PostScript Text
3' UTR -662.242715-0.244 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
IPR019325 - NEDD4/BSD2

Pfam Domains:
PF10176 - Protein of unknown function (DUF2370)

ModBase Predicted Comparative 3D Structure on Q9BT67
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-  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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0050699 WW domain binding

Biological Process:
GO:0002761 regulation of myeloid leukocyte differentiation
GO:0002829 negative regulation of type 2 immune response
GO:0006879 cellular iron ion homeostasis
GO:0007034 vacuolar transport
GO:0010629 negative regulation of gene expression
GO:0030001 metal ion transport
GO:0031398 positive regulation of protein ubiquitination
GO:0032410 negative regulation of transporter activity
GO:0032713 negative regulation of interleukin-4 production
GO:0042130 negative regulation of T cell proliferation
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0045619 regulation of lymphocyte differentiation
GO:0045732 positive regulation of protein catabolic process
GO:0048294 negative regulation of isotype switching to IgE isotypes
GO:0048302 regulation of isotype switching to IgG isotypes
GO:0050728 negative regulation of inflammatory response
GO:0051224 negative regulation of protein transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005938 cell cortex
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030425 dendrite
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK075495 - Homo sapiens cDNA PSEC0192 fis, clone HEMBA1000675.
AK315481 - Homo sapiens cDNA, FLJ96543, Homo sapiens likely ortholog of mouse Nedd4 WW binding protein 5 (N4WBP5), mRNA.
AY192728 - Homo sapiens breast cancer-associated protein SGA-1M mRNA, complete cds.
AK075524 - Homo sapiens cDNA PSEC0223 fis, clone HEMBA1005628, highly similar to Nedd4 family interacting protein 1.
AB097010 - Homo sapiens mRNA for putative NFkB activating protein, complete cds, clone: 164.
AB097037 - Homo sapiens mRNA for putative MAPK activating protein, complete cds, clone: PM13.
BC004317 - Homo sapiens Nedd4 family interacting protein 1, mRNA (cDNA clone MGC:10924 IMAGE:3628100), complete cds.
JD362014 - Sequence 343038 from Patent EP1572962.
JD140500 - Sequence 121524 from Patent EP1572962.
HQ447371 - Synthetic construct Homo sapiens clone IMAGE:100070692; CCSB004284_02 Nedd4 family interacting protein 1 (NDFIP1) gene, encodes complete protein.
KJ899652 - Synthetic construct Homo sapiens clone ccsbBroadEn_09046 NDFIP1 gene, encodes complete protein.
AL832993 - Homo sapiens mRNA; cDNA DKFZp666L233 (from clone DKFZp666L233).
AK124884 - Homo sapiens cDNA FLJ42894 fis, clone BRHIP3008606.
JD259186 - Sequence 240210 from Patent EP1572962.
JD077509 - Sequence 58533 from Patent EP1572962.
JD261942 - Sequence 242966 from Patent EP1572962.
JD432019 - Sequence 413043 from Patent EP1572962.
JD273785 - Sequence 254809 from Patent EP1572962.
JD302528 - Sequence 283552 from Patent EP1572962.
JD196656 - Sequence 177680 from Patent EP1572962.
JD389616 - Sequence 370640 from Patent EP1572962.
JD183372 - Sequence 164396 from Patent EP1572962.
JD065700 - Sequence 46724 from Patent EP1572962.
JD267497 - Sequence 248521 from Patent EP1572962.
JD202378 - Sequence 183402 from Patent EP1572962.
JD290739 - Sequence 271763 from Patent EP1572962.
JD503966 - Sequence 484990 from Patent EP1572962.
JD541112 - Sequence 522136 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDB8, D3DQF0, N4WBP5, NFIP1_HUMAN, NM_030571, NP_085048, PSEC0192, PSEC0223, Q658T8, Q8N2E3, Q8N2F9, Q9BT67
UCSC ID: uc003lmi.4
RefSeq Accession: NM_030571
Protein: Q9BT67 (aka NFIP1_HUMAN)
CCDS: CCDS4273.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_030571.3
exon count: 8CDS single in 3' UTR: no RNA size: 3599
ORF size: 666CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1532.00frame shift in genome: no % Coverage: 99.94
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.