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    Nipbl NIPBL cohesin loading factor [ Mus musculus (house mouse) ]

    Gene ID: 71175, updated on 9-Dec-2024

    Summary

    Official Symbol
    Nipblprovided by MGI
    Official Full Name
    NIPBL cohesin loading factorprovided by MGI
    Primary source
    MGI:MGI:1913976
    See related
    Ensembl:ENSMUSG00000022141 AllianceGenome:MGI:1913976
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Idn3
    Summary
    Enables cohesin loader activity; mediator complex binding activity; and promoter-specific chromatin binding activity. Involved in mitotic sister chromatid segregation; positive regulation of neuron migration; and regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including embryonic viscerocranium morphogenesis; fat cell differentiation; and positive regulation of ossification. Located in chromatin and nucleus. Part of integrator complex. Is expressed in several structures, including genitourinary system; integumental system; limb; nervous system; and nose. Used to study Cornelia de Lange syndrome and Cornelia de Lange syndrome 1. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome and Cornelia de Lange syndrome 1. Orthologous to human NIPBL (NIPBL cohesin loading factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 9.6), CNS E11.5 (RPKM 8.2) and 27 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Nipbl in Genome Data Viewer
    Location:
    15 A1; 15 3.82 cM
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (8319308..8494799, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (8289824..8465315, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene ciliogenesis and planar polarity effector 1 Neighboring gene STARR-seq mESC enhancer starr_37896 Neighboring gene STARR-seq mESC enhancer starr_37897 Neighboring gene predicted gene, 24144 Neighboring gene predicted gene, 41265 Neighboring gene uncharacterized LOC102634078 Neighboring gene STARR-seq mESC enhancer starr_37899 Neighboring gene STARR-positive B cell enhancer ABC_E2437 Neighboring gene STARR-seq mESC enhancer starr_37901 Neighboring gene predicted gene, 31282 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:8462039-8462148 Neighboring gene predicted gene, 49249

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • 4921518A06Rik, 4933421G18Rik

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromo shadow domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromo shadow domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables cohesin loader activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables cohesin loader activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone deacetylase binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables mediator complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in DNA damage response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in brain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to X-ray IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to X-ray ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cognition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cognition ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in developmental growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in developmental growth ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in digestive tract development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ear morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within embryonic cranial skeleton morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic digestive tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digestive tract morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic forelimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in embryonic viscerocranium morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within embryonic viscerocranium morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of mitotic sister chromatid cohesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in establishment of protein localization to chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in external genitalia morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in external genitalia morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in eye morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in eye morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in face morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in face morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in forelimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in gallbladder development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in gallbladder development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heart morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in heart morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in maintenance of mitotic sister chromatid cohesion ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in maintenance of mitotic sister chromatid cohesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mitotic sister chromatid cohesion ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in mitotic sister chromatid segregation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in outflow tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in outflow tract morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of developmental growth ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of embryonic development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of hair cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of hair cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in replication-born double-strand break repair via sister chromatid exchange IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in uterus morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in uterus morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of SMC loading complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of SMC loading complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of Scc2-Scc4 cohesin loading complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of Scc2-Scc4 cohesin loading complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of Scc2-Scc4 cohesin loading complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    part_of integrator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    nipped-B-like protein
    Names
    Nipped-B homolog
    SCC2 homolog
    delangin homolog

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_027707.3NP_081983.2  nipped-B-like protein isoform a

      See identical proteins and their annotated locations for NP_081983.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (a) encodes the longer isoform (a).
      Source sequence(s)
      AJ627033, AK078435, AK135347, AV246194, BC055787
      Consensus CDS
      CCDS37035.1
      UniProtKB/Swiss-Prot
      Q6KC78, Q6KCD5, Q7TNS4, Q8BKV4, Q8CES9, Q9CUC6
      Related
      ENSMUSP00000059385.7, ENSMUST00000052965.8
      Conserved Domains (5) summary
      PTZ00121
      Location:4761099
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam11029
      Location:146214
      DAZAP2; DAZ associated protein 2 (DAZAP2)
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22702448
      Nipped-B_C; Sister chromatid cohesion C-terminus
    2. NM_201232.2NP_957684.1  nipped-B-like protein isoform b

      See identical proteins and their annotated locations for NP_957684.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (b) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC158971, AJ640138, AK078435, AK135347, AV246194, BC055787
      UniProtKB/Swiss-Prot
      Q6KCD5
      Conserved Domains (5) summary
      pfam07223
      Location:113307
      DUF1421; Protein of unknown function (DUF1421)
      pfam08648
      Location:10971154
      DUF1777; Protein of unknown function (DUF1777)
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22702448
      Nipped-B_C; Sister chromatid cohesion C-terminus
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000081.7 Reference GRCm39 C57BL/6J

      Range
      8319308..8494799 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006519994.4XP_006520057.1  nipped-B-like protein isoform X1

      See identical proteins and their annotated locations for XP_006520057.1

      UniProtKB/Swiss-Prot
      Q6KC78, Q6KCD5, Q7TNS4, Q8BKV4, Q8CES9, Q9CUC6
      Conserved Domains (5) summary
      PTZ00121
      Location:4761099
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam11029
      Location:146214
      DAZAP2; DAZ associated protein 2 (DAZAP2)
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22702448
      Nipped-B_C; Sister chromatid cohesion C-terminus
    2. XM_006519995.2XP_006520058.1  nipped-B-like protein isoform X1

      See identical proteins and their annotated locations for XP_006520058.1

      UniProtKB/Swiss-Prot
      Q6KC78, Q6KCD5, Q7TNS4, Q8BKV4, Q8CES9, Q9CUC6
      Conserved Domains (5) summary
      PTZ00121
      Location:4761099
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam11029
      Location:146214
      DAZAP2; DAZ associated protein 2 (DAZAP2)
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22702448
      Nipped-B_C; Sister chromatid cohesion C-terminus
    3. XM_006519996.5XP_006520059.1  nipped-B-like protein isoform X2

      Conserved Domains (5) summary
      PTZ00121
      Location:4761099
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam11029
      Location:146214
      DAZAP2; DAZ associated protein 2 (DAZAP2)
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22702448
      Nipped-B_C; Sister chromatid cohesion C-terminus

    RNA

    1. XR_004938871.1 RNA Sequence