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NIPBL Gene

protein-coding   GIFtS: 61
GCID: GC05P036876

Nipped-B Homolog (Drosophila)

  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
Nipped-B Homolog (Drosophila)1 2     IDN3-B2
IDN32 3     Scc22
SCC2 Homolog2 3     delangin2
CDLS12 5     Nipped-B-Like Protein2
Sister Chromatid Cohesion 2 Homolog (Yeast)1     Sister Chromatid Cohesion 2 Homolog2
CDLS2     Delangin3

External Ids:    HGNC: 288621   Entrez Gene: 258362   Ensembl: ENSG000001641907   OMIM: 6086675   UniProtKB: Q6KC793   

Export aliases for NIPBL gene to outside databases

Previous GC identifer: GC05P036912


(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 NIPBL Gene:
This gene encodes the homolog of the Drosophila melanogaster Nipped-B gene product and fungal Scc2-type sister
chromatid cohesion proteins. The Drosophila protein facilitates enhancer-promoter communication of remote
enhancers and plays a role in developmental regulation. It is also homologous to a family of chromosomal adherins
with broad roles in sister chromatid cohesion, chromosome condensation, and DNA repair. The human protein has a
bipartite nuclear targeting sequence and a putative HEAT repeat. Condensins, cohesins and other complexes with
chromosome-related functions also contain HEAT repeats. Mutations in this gene result in Cornelia de Lange
syndrome, a disorder characterized by dysmorphic facial features, growth delay, limb reduction defects, and
mental retardation. Two transcript variants encoding different isoforms have been found for this gene. (provided
by RefSeq, Jul 2008)

GeneCards Summary for NIPBL Gene:
NIPBL (Nipped-B homolog (Drosophila)) is a protein-coding gene. Diseases associated with NIPBL include nipbl-related cornelia de lange syndrome, and limb reduction defect. GO annotations related to this gene include chromatin binding and protein N-terminus binding.

UniProtKB/Swiss-Prot: NIPBL_HUMAN, Q6KC79
Function: Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by
interacting with the cohesin complex (By similarity)

Gene Wiki entry for NIPBL 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_000005.10  NT_006576.17  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NIPBL gene promoter:
         MAZR   FOXO3   AP-2gamma   Egr-4   C/EBPalpha   CHOP-10   FOXO3a   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): NIPBL promoter sequence
   Search Chromatin IP Primers for NIPBL

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


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

Entrez Gene cytogenetic band: 5p13.2   Ensembl cytogenetic band:  5p13.2   HGNC cytogenetic band: 5p13.2

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

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P036876:  view genomic region     (about GC identifiers)

Start:
36,876,861 bp from pter      End:
37,066,515 bp from pter
Size:
189,655 bases      Orientation:
plus 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NIPBL_HUMAN, Q6KC79 (See protein sequence)
Recommended Name: Nipped-B-like protein  
Size: 2804 amino acids; 316051 Da
Subunit: Interacts directly with CBX5 via the PxVxL motif
Developmental stage: In embryos, it is expressed in developing limbs and later in cartilage primordia of the ulna
and of various hand bones. Sites of craniofacial expression include the cartilage primordium of the basioccipital
and basisphenoid skull bones and elsewhere in the head and face, including a region encompassing the mesenchyme
adjacent to the cochlear canal. Also expressed in the spinal column, notochord and surface ectoderm sclerotome
and what seem to be migrating myoblasts. Expressed in the developing heart in the atrial and ventricular
myocardium and in the ventricular tubeculae but absent in the endocardial cushions. Also expressed in the
developing esophagus, trachea and midgut loops, in the bronchi of the lung and in the tubules of the metanephros.
Expression in organs and tissues not typically affected in CDL (e.g. the developing trachea, bronchi, esophagus,
heart and kidney) may reflect a bias towards underreporting of more subtle aspects of the phenotype or problems
that typically present later in life. Expressed in the mesenchyme surrounding the cochlear canal possibly
reflecting the hearing impairment commonly found. Weakly or not expressed in embryonic brain
Sequence caution: Sequence=AAH33847.1; Type=Erroneous initiation; Sequence=BAA77335.1; Type=Miscellaneous
discrepancy; Note=Chimeric cDNA; Sequence=BAA77349.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA;
Sequence=BAC86701.1; Type=Erroneous initiation; Sequence=CAE45790.1; Type=Frameshift; Positions=278;
Secondary accessions: Q6KCD6 Q6N080 Q6ZT92 Q7Z2E6 Q8N4M5 Q9Y6Y3 Q9Y6Y4
Alternative splicing: 3 isoforms:  Q6KC79-1   Q6KC79-2   Q6KC79-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NIPBL: NX_Q6KC79

Explore proteomics data for NIPBL at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins (2 alternative transcripts): 
    NP_056199.2  NP_597677.2  

    ENSEMBL proteins: 
     ENSP00000282516   ENSP00000406266   ENSP00000421504  
    Reactome Protein details: Q6KC79

    NIPBL Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for NIPBL

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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:
     IPR011989 ARM-like
     IPR026003 Cohesin_HEAT
     IPR024986 Nipped-B_C
     IPR016024 ARM-type_fold

    Graphical View of Domain Structure for InterPro Entry Q6KC79

    ProtoNet protein and cluster: Q6KC79

    1 Blocks protein domain: IPB000357 HEAT repeat

    UniProtKB/Swiss-Prot: NIPBL_HUMAN, Q6KC79
    Domain: Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow
    domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the
    chromoshadow domain
    Similarity: Belongs to the SCC2/Nipped-B family
    Similarity: Contains 5 HEAT repeats


    NIPBL 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: NIPBL_HUMAN, Q6KC79
    Function: Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by
    interacting with the cohesin complex (By similarity)

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IEA--
    GO:0005488binding ----
    GO:0005515protein binding IPI16682347
    GO:0008022protein C-terminus binding IPI17577209
    GO:0036033mediator complex binding IEA--
         
    NIPBL for ontologies           About GeneDecksing


    Phenotypes:
         13 MGI mutant phenotypes (inferred from 1 allele(MGI details for Nipbl):
     adipose tissue  behavior/neurological  cardiovascular system  cellular  craniofacial 
     growth/size/body  hearing/vestibular/ear  immune system  limbs/digits/tail  mortality/aging 
     nervous system  skeleton  vision/eye 

    NIPBL for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NIPBL
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NIPBL
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NIPBL

    miRNA
    Products:
        
    miRTarBase miRNAs that target NIPBL:
    hsa-let-7a-5p (MIRT052641), hsa-mir-183-5p (MIRT047113), hsa-mir-18a-3p (MIRT040938), hsa-mir-210-3p (MIRT003175), hsa-mir-421 (MIRT016135), hsa-mir-30b-5p (MIRT046116), hsa-mir-21-5p (MIRT030681), hsa-let-7b-5p (MIRT032211)

    Block miRNA regulation of human, mouse, rat NIPBL using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NIPBL (see all 127):
    hsa-miR-194* hsa-miR-323-3p hsa-miR-4254 hsa-miR-607 hsa-miR-3607-3p hsa-miR-300 hsa-miR-376b hsa-miR-188-5p
    SwitchGear 3'UTR luciferase reporter plasmidNIPBL 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat NIPBL

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    GenScript: all cDNA clones in your preferred vector (see all 2): NIPBL (NM_133433)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NIPBL
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat NIPBL

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NIPBL


    (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
    NIPBL_HUMAN, Q6KC79: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    endoplasmic reticulum2
    plasma membrane2
    mitochondrion1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA16802858
    GO:0005654nucleoplasm TAS--
    GO:0032116SMC loading complex IDA16682347
    GO:0070062extracellular vesicular exosome IDA19056867

    NIPBL 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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    SuperPaths for NIPBL About    
    See pathways by source

    SuperPathContained pathways About
    1Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    M Phase0.62
    Cell Cycle0.90
    2Mitotic Telophase/Cytokinesis
    Mitotic Telophase/Cytokinesis
    Cohesin Loading onto Chromatin0.00

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for NIPBL
        Cohesin Loading onto Chromatin



    NIPBL for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NIPBL
    Interactions:

        Search GeneGlobe Interaction Network for NIPBL

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

    Selected Interacting proteins for NIPBL (Q6KC792, 3 ENSP000002825164) via UniProtKB, MINT, STRING, and/or I2D (see all 842)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOC2Q96KP12, 3MINT-7945693 MINT-7947479 I2D: score=2 
    SMC1AQ146832, ENSP000003234214MINT-7945693 MINT-7947479 STRING: ENSP00000323421
    FEN1P397482, ENSP000003054804MINT-7945693 MINT-7947479 STRING: ENSP00000305480
    RFC3P409382, ENSP000003694114MINT-7945693 MINT-7947479 STRING: ENSP00000369411
    CDC5LQ994592, ENSP000003605324MINT-7945693 MINT-7947479 STRING: ENSP00000360532
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 35):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA18854353
    GO:0000278mitotic cell cycle TAS--
    GO:0001656metanephros development NAS15146185
    GO:0003007heart morphogenesis IMP8291537
    GO:0003151outflow tract morphogenesis IMP19242925

    NIPBL 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 NIPBL



    (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,
    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 NIPBL gene (2 alternative transcripts): 
    NM_015384.4  NM_133433.3  

    Unigene Cluster for NIPBL:

    Nipped-B homolog (Drosophila)
    Hs.481927  [show with all ESTs]
    Unigene Representative Sequence: NM_015384
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000282516(uc003jkl.4 uc003jkk.4) ENST00000448238 ENST00000505998
    ENST00000504430(uc003jkm.1) ENST00000503274 ENST00000509429 ENST00000514335(uc003jkn.3)
    ENST00000513819
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat NIPBL using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NIPBL (see all 127):
    hsa-miR-194* hsa-miR-323-3p hsa-miR-4254 hsa-miR-607 hsa-miR-3607-3p hsa-miR-300 hsa-miR-376b hsa-miR-188-5p
    SwitchGear 3'UTR luciferase reporter plasmidNIPBL 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for NIPBL
    Predesigned siRNA for gene silencing in human, mouse, rat NIPBL
    Clone
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    OriGene ORF clones in mouse, rat for NIPBL
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): NIPBL (NM_133433)
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat NIPBL
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NIPBL
      QuantiTect SYBR Green Assays in human, mouse, rat NIPBL
      QuantiFast Probe-based Assays in human, mouse, rat NIPBL

    Additional mRNA sequence: 

    AJ627032.1 AJ640137.1 AK002065.1 AK022659.1 AK023416.1 AK126804.1 AK290347.1 AL137726.1 
    AY726600.1 BC032711.1 BC033847.1 BC131490.1 BC146821.1 BX538177.1 BX538178.1 BX640644.1 

    18 DOTS entries:

    DT.97794930  DT.101957330  DT.453704  DT.97760558  DT.95208058  DT.100892259  DT.92433347  DT.100892249 
    DT.86846283  DT.91996418  DT.120822286  DT.120822287  DT.120822352  DT.429552  DT.86858693  DT.92009977 
    DT.92433335  DT.97774789 

    Selected AceView cDNA sequences (see all 237):

    CB162827 AW772083 CD244796 CA312640 BM676996 AI352504 AA909045 AI566250 
    Z45821 AW665234 BM449960 AK126804 BF197994 NM_015384 NM_133433 BE047147 
    AW015116 AW058609 AA782599 BX092252 CA445139 BQ020447 BQ929549 AK023416 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for NIPBL (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^
    SP1:                                                                          -                                                                                 
    SP2:                                                                          -                                                                                 
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40a · 40b ^ 41 ^ 42a · 42b ^ 43 ^ 44 ^ 45a · 45b · 45c ^ 46 ^
    SP1:        -                                                                                                     -                                             
    SP2:        -                                                                                                     -                                             
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                              -                 -                           

    ExUns: 47a · 47b · 47c ^ 48a · 48b
    SP1:        -     -               
    SP2:                              
    SP3:                              
    SP4:              -               
    SP5:                              


    ECgene alternative splicing isoforms for NIPBL

    (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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    NIPBL expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAGTATCTAT
    NIPBL Expression
    About this image


    NIPBL expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Prechondrocytic Mesenchymal Cells Vertebral Body
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Prechondrocytic Mesenchymal Cells Vertebral Body
     
     Somite (Muscoskeletal System)    fully expand to see all 2 entries
             Lumbar Mesenchymal Sclerotome
     
     Neural Tube (Nervous System)
             Telencephalon
     
     Head Mesenchyme (Muscoskeletal System)
             Head Mesenchyme
    NIPBL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NIPBL Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.481927

    UniProtKB/Swiss-Prot: NIPBL_HUMAN, Q6KC79
    Tissue specificity: Widely expressed. Highly expressed in heart, skeletal muscle, fetal and adult liver, fetal and
    adult kidney. Expressed at intermediates level in thymus, placenta, peripheral leukocyte and small intestine.
    Weakly or not expressed in brain, colon, spleen and lung

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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 and fungi.

    Orthologs for NIPBL gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nipbl1 , 5 Nipped-B homolog (Drosophila)1, 5 92.63(n)1
    96.89(a)1
      15 (3.82 cM)5
    711751  NM_027707.31  NP_081983.21 
     82912255 
    chicken
    (Gallus gallus)
    Aves LOC4274391 Nipped-B homolog-like 84.36(n)
    89.7(a)
      427439  XM_425012.4  XP_425012.3 
    lizard
    (Anolis carolinensis)
    Reptilia NIPBL6
    Nipped-B homolog (Drosophila)
    88(a)
    1 ↔ 1
    GL343241.1(1064207-1169539)
    African clawed frog
    (Xenopus laevis)
    Amphibia BU911385.12   -- 76.08(n)    BU911385.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570653682   -- 76.33(n)    57065368 
    fruit fly
    (Drosophila melanogaster)
    Insecta Nipped-B1 Nipped-B 51.35(n)
    43.53(a)
      3355136  NM_001169581.2  NP_001163052.1 
    worm
    (Caenorhabditis elegans)
    Secernentea pqn-856
    Protein PQN-85 (pqn-85) mRNA, complete cds
    27(a)
    1 ↔ 1
    II(240717-255182) WBGene00004166
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SCC2(YDR180W)4 Subunit of cohesin loading factor (Scc2p-Scc4p), a more   --   4(821295-825776) 851761  NP_010466.1 


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

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

    (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 NIPBL (see all 3498)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0216014
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216012 D V mis40--------
    VAR_0216084
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216082 Y H mis40--------
    VAR_0216044
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216042 R H mis40--------
    VAR_0216034
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216032 R C mis40--------
    VAR_0195204
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0195202 L R mis40--------
    VAR_0215994
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0215992 L P mis40--------
    VAR_0216024
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216022 R T mis40--------
    VAR_0216074
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216072 A T mis40--------
    VAR_0361644
    A breast cancer sample4--see VAR_0361642 E K mis40--------
    VAR_0216054
    Cornelia de Lange syndrome 1 (CDLS1)4--see VAR_0216052 G R mis40--------

    HapMap Linkage Disequilibrium report for NIPBL (36876861 - 37066515 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for NIPBL:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2525217CNV Deletion19546169
    nsv880502CNV Loss21882294
    dgv6036n71CNV Loss21882294
    nsv525478CNV Loss19592680
    nsv830264CNV Loss17160897

    Human Gene Mutation Database (HGMD): NIPBL
    Locus Specific Mutation Databases (LSDB): NIPBL

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608667   
    OMIM disorders: 122470  
    UniProtKB/Swiss-Prot: NIPBL_HUMAN, Q6KC79
  • Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470]: A form of Cornelia de Lange syndrome, a clinically
    heterogeneous developmental disorder associated with malformations affecting multiple systems. Characterized by
    facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal
    dysfunction and cardiac, ophthalmologic and genitourinary anomalies. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • Selected diseases for NIPBL (see all 22):    
    About MalaCards
    nipbl-related cornelia de lange syndrome    limb reduction defect    5p13 microduplication syndrome    cornelia de lange syndrome 1
    cornelia de lange syndrome    sc phocomelia syndrome    hypertropia    roberts syndrome
    developmental disabilities    lymphedema    congenital diaphragmatic hernia    mental retardation
    intellectual disability    breast and colorectal cancer    cervicitis    obesity
    colorectal cancer    hiv-1    cerebritis    multiple myeloma

    4 diseases from the University of Copenhagen DISEASES database for NIPBL:
    Cornelia de Lange syndrome     Roberts syndrome     Intellectual disability     SC phocomelia syndrome

    NIPBL for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for NIPBL gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cornelia de lange syndrome 98.3 11 15373324 (1), 16799922 (1), 16802858 (1), 17965872 (1) (see all 11)
    developmental disabilities 73.1 2 15373324 (1), 11391654 (1)
    mental retardation 72.7 1 16213388 (1)
    growth retardation 59.7 3 16802858 (1), 17221863 (1), 16213388 (1)
    chromosomal aberrations 36.6 1 11391654 (1)

    GeneTests: NIPBL
    GeneReviews: NIPBL
    Genetic Association Database (GAD): NIPBL
    Human Genome Epidemiology (HuGE) Navigator: NIPBL (2 documents)

    Export disorders for NIPBL 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 NIPBL gene, integrated from 10 sources (see all 94):
    (articles sorted by number of sources associating them with NIPBL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. (PubMed id 20358602)1, 2, 4, 9 Pie J....Ramos F.J. (Am. J. Med. Genet. A 2010)
    2. NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome. (PubMed id 15146185)1, 2, 3 Tonkin E.T.... Strachan T. (Nat. Genet. 2004)
    3. Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. (PubMed id 15146186)1, 2, 3 Krantz I.D....Jackson L.G. (Nat. Genet. 2004)
    4. Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation. (PubMed id 20562864)1, 2 Nozawa R.S.... Obuse C. (Nat. Cell Biol. 2010)
    5. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)1, 4 Jugessur A....Murray J.C. (PLoS ONE 2010)
    6. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (Nat. Biotechnol. 2006)
    7. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    8. The mammalian heterochromatin protein 1 binds diverse nuclear proteins through a common motif that targets the chromoshadow domain. (PubMed id 15882967)1, 2 Lechner M.S.... Rauscher F.J. III (Biochem. Biophys. Res. Commun. 2005)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 25836 HGNC: 28862 AceView: NIPBL Ensembl:ENSG00000164190 euGenes: HUgn25836
    ECgene: NIPBL H-InvDB: NIPBL

    (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 NIPBL Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for NIPBL Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=NIPBL[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NIPBL gene:
    Search GeneIP for patents involving NIPBL

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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