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NUFIP1 Gene

protein-coding   GIFtS: 50
GCID: GC13M045513

Nuclear Fragile X Mental Retardation Protein Interacting...

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Nuclear Fragile X Mental Retardation Protein Interacting Protein 11 2
Nuclear FMRP-Interacting Protein 12 3
NUFIP2 5
bA540M5.12
Nuclear Fragile X Mental Retardation-Interacting Protein 12

External Ids:    HGNC: 80571   Entrez Gene: 267472   Ensembl: ENSG000000836357   OMIM: 6043545   UniProtKB: Q9UHK03   

Export aliases for NUFIP1 gene to outside databases

Previous GC identifers: GC13M043513 GC13M039499 GC13M044450 GC13M043311 GC13M044411 GC13M026315


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NUFIP1 Gene:
This gene encodes a nuclear RNA binding protein that contains a C2H2 zinc finger motif and a nuclear localization
signal. This protein is associated with the nuclear matrix in perichromatin fibrils and, in neurons, localizes to
the cytoplasm in association with endoplasmic reticulum ribosomes. This protein interacts with the fragile X
mental retardation protein (FMRP), the tumor suppressor protein BRCA1, upregulates RNA polymerase II
transcription, and is involved in box C/D snoRNP biogenesis. A pseudogene of this gene resides on chromosome
6q12. (provided by RefSeq, Feb 2012)

GeneCards Summary for NUFIP1 Gene:
NUFIP1 (nuclear fragile X mental retardation protein interacting protein 1) is a protein-coding gene. Diseases associated with NUFIP1 include mental retardation, and intellectual disability. GO annotations related to this gene include RNA binding and protein binding, bridging.

UniProtKB/Swiss-Prot: NUFP1_HUMAN, Q9UHK0
Function: Binds RNA

Gene Wiki entry for NUFIP1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000013.11  NC_018924.2  NT_024524.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the NUFIP1 gene promoter:
         AP-2rep   SRF   Max1   SRF (504 AA)   CUTL1   PPAR-gamma1   GATA-6   HSF2   PPAR-gamma2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNUFIP1 promoter sequence
   Search Chromatin IP Primers for NUFIP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NUFIP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q14   Ensembl cytogenetic band:  13q14.12   HGNC cytogenetic band: 13q14

NUFIP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NUFIP1 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M045513:  view genomic region     (about GC identifiers)

Start:
45,513,384 bp from pter      End:
45,563,618 bp from pter
Size:
50,235 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: NUFP1_HUMAN, Q9UHK0 (See protein sequence)
Recommended Name: Nuclear fragile X mental retardation-interacting protein 1  
Size: 495 amino acids; 56300 Da
Subunit: Interacts with FMR1
Sequence caution: Sequence=AAH17745.1; Type=Erroneous initiation;
Secondary accessions: Q8WVM5 Q96SG1

Explore the universe of human proteins at neXtProt for NUFIP1: NX_Q9UHK0

Explore proteomics data for NUFIP1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NUFIP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036477.2  
    ENSEMBL proteins: 
     ENSP00000368459  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR019496 NUFIP1_cons_dom
     IPR015880 Znf_C2H2-like
     IPR007087 Znf_C2H2
     IPR022755 Znf_C2H2_jaz

    Graphical View of Domain Structure for InterPro Entry Q9UHK0

    ProtoNet protein and cluster: Q9UHK0

    UniProtKB/Swiss-Prot: NUFP1_HUMAN, Q9UHK0
    Similarity: Contains 1 C2H2-type zinc finger


    NUFIP1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NUFP1_HUMAN, Q9UHK0
    Function: Binds RNA

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS15107825
    GO:0003723RNA binding IDA10556305
    GO:0005515protein binding IPI10556305
    GO:0030515contributes to snoRNA binding IDA17636026
    GO:0030674protein binding, bridging IPI17636026
         
    NUFIP1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NUFIP1
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    miRNA
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    miRTarBase miRNAs that target NUFIP1:
    hsa-mir-215-5p (MIRT024863), hsa-mir-192-5p (MIRT026907)

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    Selected qRT-PCR Assays for microRNAs that regulate NUFIP1 (see all 10):
    hsa-miR-4254 hsa-miR-448 hsa-miR-548e hsa-miR-548v hsa-miR-545 hsa-miR-4275 hsa-miR-153 hsa-miR-548a-3p
    SwitchGear 3'UTR luciferase reporter plasmidNUFIP1 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NUFP1_HUMAN, Q9UHK0: Nucleus. Note=Distributed in the nucleus in a dot-like pattern
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton4
    cytosol4

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005726perichromatin fibrils IDA12941608
    GO:0005730nucleolus IDA--
    GO:0008023transcription elongation factor complex IDA15107825
    GO:0016363nuclear matrix IDA12941608

    NUFIP1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NUFIP1
    Interactions:

        GeneGlobe Interaction Network for NUFIP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for NUFIP1 (Q9UHK01, 2, 3 ENSP000003684594) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NHP2L1P557691, 3EBI-2563549,EBI-712228 I2D: score=5 
    YWHAZP631042, 3, ENSP000003095034MINT-3319708 I2D: score=1 STRING: ENSP00000309503
    BRCA1P383983, ENSP000003502834I2D: score=3 STRING: ENSP00000350283
    CCNT1O605633, ENSP000002619004I2D: score=3 STRING: ENSP00000261900
    RUVBL2Q9Y2303, ENSP000002214134I2D: score=1 STRING: ENSP00000221413
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000492box C/D snoRNP assembly IMP17636026
    GO:0006396RNA processing TAS10556305
    GO:0045944positive regulation of transcription from RNA polymerase II promoter IMP15107825

    NUFIP1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NUFIP1 (NUFP1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for NUFIP1 gene: 
    NM_012345.2  

    Unigene Cluster for NUFIP1:

    Nuclear fragile X mental retardation protein interacting protein 1
    Hs.525006  [show with all ESTs]
    Unigene Representative Sequence: NM_012345
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000379161(uc001uzp.2)
    miRNA
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    hsa-miR-4254 hsa-miR-448 hsa-miR-548e hsa-miR-548v hsa-miR-545 hsa-miR-4275 hsa-miR-153 hsa-miR-548a-3p
    SwitchGear 3'UTR luciferase reporter plasmidNUFIP1 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat NUFIP1
      QuantiFast Probe-based Assays in human, mouse, rat NUFIP1

    Additional mRNA sequence: 

    AF159548.1 AK314242.1 BC001436.1 BC017745.1 

    4 DOTS entries:

    DT.311423  DT.95265455  DT.121310919  DT.99993491 

    Selected AceView cDNA sequences (see all 78):

    AA377043 CA424844 AA300838 AW297501 AW293648 BX374594 BM722745 AA732677 
    AA300673 AA313568 BC017745 AI216506 BG188808 BX283859 AA214642 CB306417 
    AI470636 CD557235 AI220307 AI445539 AI168720 AI493868 BG771372 BC001436 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NUFIP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NUFIP1 Expression
    About this image

    NUFIP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NUFIP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.525006

    UniProtKB/Swiss-Prot: NUFP1_HUMAN, Q9UHK0
    Tissue specificity: Expressed in spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral blood
    leukocyte, heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for NUFIP1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nufip11 , 5 nuclear fragile X mental retardation protein interacting more1, 5 79.92(n)1
    72.67(a)1
      14 (40.35 cM)5
    272751  NM_013745.51  NP_038773.11 
     761108915 
    chicken
    (Gallus gallus)
    Aves NUFIP16
    Gallus gallus nuclear fragile X mental retardation...
    36(a)
    1 ↔ 1
    1(166904655-166927469)
    lizard
    (Anolis carolinensis)
    Reptilia NUFIP16
    nuclear fragile X mental retardation protein inter...
    36(a)
    1 ↔ 1
    GL343395.1(591871-615633)
    African clawed frog
    (Xenopus laevis)
    Amphibia AW645513.12   -- 78.78(n)    AW645513.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1714761 zgc:171476 54.27(n)
    50.53(a)
      334271  NM_001114886.1  NP_001108358.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Nufip6
    Nufip
    19(a)
    1 ↔ 1
    3L(18739711-18741467)


    ENSEMBL Gene Tree for NUFIP1 (if available)
    TreeFam Gene Tree for NUFIP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NUFIP1 gene

    NUFIP1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NUFIP1
    PGOHUM00000243235


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NUFIP1 (see all 997)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs790489841,2
    C--26315873(+) AAGCC-/TTATAA 2 -- ut310--------
    rs11753861,2
    C,F,H--26457815(+) AGCACA/CCCAGA 1 -- ds50017Minor allele frequency- C:0.02NS NA WA 626
    rs1831948671,2
    --26457847(+) AGAAAG/TCAATC 1 -- ds50010--------
    rs1458931251,2
    --26457918(+) CCAGGG/TATTAA 1 -- ds50010--------
    rs1387756851,2
    --26457939(+) AAATCA/GTATCT 1 -- ds50010--------
    rs1855186491,2
    --26458068(+) GTAATC/TACTAA 1 -- ds50010--------
    rs2001956431,2
    C--26458134(+) AAAAAA/TAACAA 1 -- ds50010--------
    rs1903093671,2
    --26458217(+) GTCCAA/CATGTT 1 -- ut310--------
    rs1821694731,2
    --26458337(+) TAAAAA/GGCACA 1 -- ut310--------
    rs575859571,2
    C,F--26458363(+) TGTAAT/AGCTTA 1 -- ut311Minor allele frequency- A:0.50WA 2

    HapMap Linkage Disequilibrium report for NUFIP1 (45513384 - 45563618 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for NUFIP1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv524788CNV Loss19592680
    dgv1578n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NUFIP1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604354    OMIM disorders: --

    5 diseases for NUFIP1:    About MalaCards
    mental retardation    intellectual disability    microcephaly    neuronitis
    prostatitis


    NUFIP1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): NUFIP1
    Human Genome Epidemiology (HuGE) Navigator: NUFIP1 (1 document)

    Export disorders for NUFIP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NUFIP1 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with NUFIP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel RNA-binding nuclear protein that interacts with the fragile X mental retardation (FMR1) protein. (PubMed id 10556305)1, 2, 3 Bardoni B.... Mandel J.-L. (Hum. Mol. Genet. 1999)
    2. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PubMed id 20201926)1, 4 Joslyn G....White R.L. (Alcohol. Clin. Exp. Res. 2010)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    4. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (Nature 2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. Assignment of NUFIP1 (nuclear FMRP interacting protein 1) gene to chromosome 13q14 and assignment of a pseudogene to chromosome 6q12. (PubMed id 10894927)1, 3 Bardoni B....Mandel J.L. (Cytogenet. Cell Genet. 2000)
    7. Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. (PubMed id 23362303)1 Wu J.H....Mozaffarian D. (Circ Cardiovasc Genet 2013)
    8. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (Sci. Signal. 2011)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    10. Systematic analysis of human protein complexes identifies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R.... Peters J.M. (Science 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 26747 HGNC: 8057 AceView: NUFIP1 Ensembl:ENSG00000083635 euGenes: HUgn26747
    ECgene: NUFIP1 H-InvDB: NUFIP1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NUFIP1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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