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    NIPBL NIPBL, cohesin loading factor [ Homo sapiens (human) ]

    Gene ID: 25836, updated on 19-Jul-2016
    Official Symbol
    NIPBLprovided by HGNC
    Official Full Name
    NIPBL, cohesin loading factorprovided by HGNC
    Primary source
    HGNC:HGNC:28862
    See related
    Ensembl:ENSG00000164190 HPRD:10560; MIM:608667; Vega:OTTHUMG00000090795
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDLS; IDN3; Scc2; CDLS1; IDN3-B
    Summary
    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]
    Orthologs
    Location:
    5p13.2
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (36876759..37065819)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (36876861..37065926)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986412 Neighboring gene NIPBL antisense RNA 1 (head to head) Neighboring gene keratin 18 pseudogene 31 Neighboring gene chromosome 5 open reading frame 42 Neighboring gene ribosomal protein S4X pseudogene 6 Neighboring gene chromosome 8 open reading frame 59 pseudogene 2

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Cornelia de Lange syndrome 1
    MedGen: CN029798 OMIM: 122470 GeneReviews: Cornelia de Lange Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    Little evidence for dosage pathogenicity (Last evaluated (2011-10-28)

    ClinGen Genome Curation PagePubMed
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2011-10-28)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, Nipped-B homolog (NIPBL), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with NIPBL is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    • Cell Cycle, organism-specific biosystem (from REACTOME)
      Cell Cycle, organism-specific biosystem
      Cell Cycle
    • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
      Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
    • Cohesin Loading onto Chromatin, organism-specific biosystem (from REACTOME)
      Cohesin Loading onto Chromatin, organism-specific biosystemIn mitotic telophase, as chromosomes decondense, cohesin complex associated with PDS5 (PDS5A and PDS5B) and WAPAL (WAPL) proteins is loaded onto chromatin (Shintomi and Hirano, 2009, Kueng et al. 200...
    • M Phase, organism-specific biosystem (from REACTOME)
      M Phase, organism-specific biosystemMitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Fin...
    • Mitotic Telophase/Cytokinesis, organism-specific biosystem (from REACTOME)
      Mitotic Telophase/Cytokinesis, organism-specific biosystemIn this final phase of mitosis, new membranes are formed around two sets of chromatids and two daughter cells are formed. The chromosomes and the spindle fibers disperse, and the fiber ring around th...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ11203, FLJ12597, FLJ13354, FLJ13648, FLJ44854, DKFZp434L1319

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromo shadow domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    mediator complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein N-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to DNA damage stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to X-ray IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    developmental growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic digestive tract morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic viscerocranium morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    external genitalia morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    face morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    fat cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    gall bladder development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    maintenance of mitotic sister chromatid cohesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    metanephros development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    mitotic sister chromatid cohesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    outflow tract morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of histone deacetylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of ossification IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of developmental growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of hair cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    uterus morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    SMC loading complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    nipped-B-like protein
    Names
    Nipped-B homolog
    SCC2 homolog
    delangin
    sister chromatid cohesion 2 homolog

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_006987.1 RefSeqGene

      Range
      4877..193937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015384.4NP_056199.2  nipped-B-like protein isoform B

      See identical proteins and their annotated locations for NP_056199.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) is alternatively spliced at the 3' end compared to transcript variant A. It encodes an isoform (B) with a shorter, distinct C-terminus, compared to isoform A.
      Source sequence(s)
      AA508213, AJ627032, AJ640137, BQ723324, CN369580
      Consensus CDS
      CCDS47198.1
      UniProtKB/Swiss-Prot
      Q6KC79
      Related
      ENSP00000406266, OTTHUMP00000221091, ENST00000448238, OTTHUMT00000366904
      Conserved Domains (3) summary
      pfam12765
      Location:17941835
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22742457
      Nipped-B_C; Sister chromatid cohesion C-terminus
      pfam12871
      Location:10871161
      PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
    2. NM_133433.3NP_597677.2  nipped-B-like protein isoform A

      See identical proteins and their annotated locations for NP_597677.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) encodes the longer isoform (A).
      Source sequence(s)
      AJ627032, CN369580
      Consensus CDS
      CCDS3920.1
      UniProtKB/Swiss-Prot
      Q6KC79
      Related
      ENSP00000282516, OTTHUMP00000116005, ENST00000282516, OTTHUMT00000207582
      Conserved Domains (3) summary
      pfam12765
      Location:17941835
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22742457
      Nipped-B_C; Sister chromatid cohesion C-terminus
      pfam12871
      Location:10871161
      PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

      Range
      36876759..37065819
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714467.2XP_006714530.1  

      Conserved Domains (3) summary
      pfam12765
      Location:17941835
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22742419
      Nipped-B_C; Sister chromatid cohesion C-terminus
      pfam12871
      Location:10871161
      PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
    2. XM_005248280.3XP_005248337.1  

      See identical proteins and their annotated locations for XP_005248337.1

      Conserved Domains (3) summary
      pfam12765
      Location:17941835
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22742457
      Nipped-B_C; Sister chromatid cohesion C-terminus
      pfam12871
      Location:10871161
      PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
    3. XM_006714468.2XP_006714531.1  

      Conserved Domains (2) summary
      pfam12765
      Location:17281769
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22082391
      Nipped-B_C; Sister chromatid cohesion C-terminus
    4. XM_017009331.1XP_016864820.1  

    5. XM_017009329.1XP_016864818.1  

    6. XM_011514015.1XP_011512317.1  

      Conserved Domains (3) summary
      pfam12765
      Location:17941835
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22742419
      Nipped-B_C; Sister chromatid cohesion C-terminus
      pfam12871
      Location:10871161
      PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
    7. XM_005248282.4XP_005248339.3  

    8. XM_017009330.1XP_016864819.1  

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      36879597..37068738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)