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

Gene ID: 71175, updated on 23-Mar-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 mediator complex binding activity and promoter-specific chromatin binding activity. Involved in cohesin loading; 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. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 1. Orthologous to human NIPBL (NIPBL cohesin loading factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 9.6), CNS E11.5 (RPKM 8.2) and 27 other tissues See more
Orthologs
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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 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 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 ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell cycle 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 ISO
Inferred from Sequence Orthology
more info
 
involved_in cognition ISO
Inferred from Sequence Orthology
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 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 ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 
involved_in eye morphogenesis ISO
Inferred from Sequence Orthology
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 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 mitotic cohesin loading IEA
Inferred from Electronic Annotation
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 
acts_upstream_of_or_within multicellular organism development 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 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 ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of gene expression 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 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 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 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 chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome 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 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)

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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_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