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    Nipbl NIPBL, cohesin loading factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 294787, updated on 9-Dec-2024

    Summary

    Official Symbol
    Nipblprovided by RGD
    Official Full Name
    NIPBL, cohesin loading factorprovided by RGD
    Primary source
    RGD:1306393
    See related
    EnsemblRapid:ENSRNOG00000056907 AllianceGenome:RGD:1306393
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    IDN3
    Summary
    Predicted to enable several functions, including chromo shadow domain binding activity; cohesin loader activity; and histone deacetylase binding activity. Predicted to be involved in several processes, including chromosome organization; embryonic morphogenesis; and reproductive structure development. Predicted to act upstream of or within several processes, including embryonic viscerocranium morphogenesis; fat cell differentiation; and positive regulation of ossification. Predicted to be located in chromatin; cytosol; and nucleoplasm. Predicted to be part of Scc2-Scc4 cohesin loading complex and integrator complex. 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
    Biased expression in Thymus (RPKM 384.2), Spleen (RPKM 264.6) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Nipbl in Genome Data Viewer
    Location:
    2q16
    Exon count:
    52
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (59126676..59314841, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (57399443..57586770, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (57508830..57676197, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene non-POU domain containing, octamer-binding, pseudogene 8 Neighboring gene ribosomal protein L9, pseudogene 4 Neighboring gene ribosomal protein L23,pseudogene 4 Neighboring gene ribosomal protein S12, pseudogene Neighboring gene high mobility group nucleosomal binding domain 2 like 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding  
    enables chromatin binding  
    enables chromo shadow domain binding  
    enables cohesin loader activity  
    enables histone deacetylase binding  
    enables mediator complex binding  
    enables promoter-specific chromatin binding  
    enables transcription corepressor activity  
    Items 1 - 25 of 44
    Process Evidence Code Pubs
    involved_in DNA damage response  
    involved_in biological_process  
    involved_in brain development  
    involved_in brain development  
    involved_in cellular response to X-ray  
    involved_in chromatin remodeling  
    involved_in cognition  
    involved_in developmental growth  
    involved_in digestive tract development  
    involved_in ear morphogenesis  
    acts_upstream_of_or_within embryonic cranial skeleton morphogenesis  
    involved_in embryonic digestive tract morphogenesis  
    involved_in embryonic forelimb morphogenesis  
    involved_in embryonic viscerocranium morphogenesis  
    acts_upstream_of_or_within embryonic viscerocranium morphogenesis  
    involved_in establishment of mitotic sister chromatid cohesion  
    involved_in establishment of protein localization to chromatin  
    involved_in external genitalia morphogenesis  
    involved_in eye morphogenesis  
    involved_in face morphogenesis  
    acts_upstream_of_or_within fat cell differentiation  
    involved_in forelimb morphogenesis  
    involved_in gallbladder development  
    acts_upstream_of_or_within heart development  
    involved_in heart morphogenesis  
    involved_in heart morphogenesis  
    involved_in maintenance of mitotic sister chromatid cohesion  
    involved_in mitotic sister chromatid cohesion  
    involved_in mitotic sister chromatid segregation  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in outflow tract morphogenesis  
    acts_upstream_of_or_within positive regulation of multicellular organism growth  
    involved_in positive regulation of neuron migration  
    acts_upstream_of_or_within positive regulation of ossification  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in protein localization  
    involved_in regulation of developmental growth  
    involved_in regulation of embryonic development  
    involved_in regulation of hair cycle  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in replication-born double-strand break repair via sister chromatid exchange  
    involved_in sensory perception of sound  
    acts_upstream_of_or_within somatic stem cell population maintenance  
    involved_in uterus morphogenesis  
    Items 1 - 25 of 44
    Component Evidence Code Pubs
    part_of SMC loading complex  
    part_of Scc2-Scc4 cohesin loading complex  
    part_of Scc2-Scc4 cohesin loading complex  
    located_in chromatin  
    located_in cytosol  
    located_in cytosol  
    part_of integrator complex  
    located_in intracellular membrane-bounded organelle  
    located_in nucleoplasm  
    located_in nucleoplasm  
    located_in nucleus  

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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_001427697.1NP_001414626.1  nipped-B-like protein isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A0A8I6AXR8
      Related
      ENSRNOP00000071473.3, ENSRNOT00000083247.3
    2. NM_001427698.1NP_001414627.1  nipped-B-like protein isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A0A8I5ZLR4, A0A8I6AXR8
      Related
      ENSRNOP00000078828.1, ENSRNOT00000097994.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      59126676..59314841 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039103537.2XP_038959465.1  nipped-B-like protein isoform X1

      UniProtKB/TrEMBL
      A0A8I6AXR8
      Conserved Domains (6) summary
      PTZ00121
      Location:5591110
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22712447
      Nipped-B_C; Sister chromatid cohesion C-terminus
      cd19953
      Location:18381872
      PDS5; HEAT repeat [structural motif]
      NF033839
      Location:593830
      PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form
    2. XM_063281521.1XP_063137591.1  nipped-B-like protein isoform X1

      UniProtKB/TrEMBL
      A0A8I6AXR8
    3. XM_039103539.2XP_038959467.1  nipped-B-like protein isoform X2

      UniProtKB/TrEMBL
      A0A8I6AXR8
      Conserved Domains (6) summary
      PTZ00121
      Location:5591110
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:18051833
      HEAT; HEAT repeat [structural motif]
      pfam12765
      Location:17881829
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:22712447
      Nipped-B_C; Sister chromatid cohesion C-terminus
      cd19953
      Location:18381872
      PDS5; HEAT repeat [structural motif]
      NF033839
      Location:593830
      PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form
    4. XM_039103540.2XP_038959468.1  nipped-B-like protein isoform X3

      UniProtKB/TrEMBL
      A0A8I6AXR8
      Conserved Domains (6) summary
      PTZ00121
      Location:448999
      PTZ00121; MAEBL; Provisional
      sd00044
      Location:16941722
      HEAT; HEAT repeat [structural motif]
      pfam12765
      Location:16771718
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:21602336
      Nipped-B_C; Sister chromatid cohesion C-terminus
      cd19953
      Location:17271761
      PDS5; HEAT repeat [structural motif]
      NF033839
      Location:482719
      PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form

    RNA

    1. XR_010063589.1 RNA Sequence

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