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

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, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 9.6), CNS E11.5 (RPKM 8.2) and 27 other tissues See more
Orthologs: human all
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Genomic context

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_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Gastrulation-stage gene expression in Nipbl[+/-] mouse embryos foreshadows the development of syndromic birth defects.
Title: Gastrulation-stage gene expression in Nipbl(+/-) mouse embryos foreshadows the development of syndromic birth defects.
Nipbl Haploinsufficiency Leads to Delayed Outflow Tract Septation and Aortic Valve Thickening.
Title: Nipbl Haploinsufficiency Leads to Delayed Outflow Tract Septation and Aortic Valve Thickening.
Depletion of Zfp609 or Nipbl from cortical neural progenitors in vivo is detrimental to neuronal migration. Zfp609 and Nipbl overlap at genomic binding sites independently of cohesin and regulate genes that control cortical neuron migration.
Title: Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration.
Nipbl transgenic mice display large atrial septal defects.
Title: Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects.
This study provides insight into the molecular pathology of Cornelia de Lange syndrome by establishing a relationship between NIPBL and HDAC8 mutations and PKR activation.
Title: NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR.
expression analysis of Smc1a and Nipbl in developing mouse embryos reveals a specific pattern in the hindbrain
Title: CyclinD1 Down-Regulation and Increased Apoptosis Are Common Features of Cohesinopathies.
Nipbl and mediator cooperatively regulate gene expression to control limb development.
Title: Nipbl and mediator cooperatively regulate gene expression to control limb development.
Nipbl+/- mutants are growth-retarded and exhibit various skeletal and craniofacial malformations.
Title: Neural crest cell-specific inactivation of Nipbl or Mau2 during mouse development results in a late onset of craniofacial defects.
In spermatocytes, Nipbl/Mau2 then relocalises to chromocenters, whereas in oocytes it remains bound to chromosomal axes throughout prophase to dictyate arrest.
Title: Localisation of the SMC loading complex Nipbl/Mau2 during mammalian meiotic prophase I.
Reduction of Nipbl is associated with Cornelia de Lange Syndrome.
Title: Reduction of Nipbl impairs cohesin loading locally and affects transcription but not cohesion-dependent functions in a mouse model of Cornelia de Lange Syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

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

Endonuclease-mediated (2)
Gene trapped (4) 1 citation
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH76750 (e-PCR)
- UniSTS:85265

Nipbl (e-PCR), detects polymorphism
- UniSTS:546895

MARC_21845-21846:1025102921:1 (e-PCR)
- UniSTS:268649

RH126661 (e-PCR)
- UniSTS:209066

D2Rat385 (e-PCR), detects polymorphism
- UniSTS:227519

Omy1296INRA (e-PCR)
- UniSTS:512481

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

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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)

NM_027707.3 → NP_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:476 → 1099

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam11029
Location:146 → 214

DAZAP2; DAZ associated protein 2 (DAZAP2)

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2270 → 2448

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_201232.2 → NP_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:113 → 307

DUF1421; Protein of unknown function (DUF1421)

pfam08648
Location:1097 → 1154

DUF1777; Protein of unknown function (DUF1777)

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2270 → 2448

Nipped-B_C; Sister chromatid cohesion C-terminus

sd00044
Location:1805 → 1833

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

NC_000081.7 Reference GRCm39 C57BL/6J

Range

8319308..8494799 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006519994.4 → XP_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:476 → 1099

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam11029
Location:146 → 214

DAZAP2; DAZ associated protein 2 (DAZAP2)

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2270 → 2448

Nipped-B_C; Sister chromatid cohesion C-terminus
XM_006519995.2 → XP_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:476 → 1099

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam11029
Location:146 → 214

DAZAP2; DAZ associated protein 2 (DAZAP2)

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2270 → 2448

Nipped-B_C; Sister chromatid cohesion C-terminus
XM_006519996.5 → XP_006520059.1 nipped-B-like protein isoform X2

Conserved Domains (5) summary

PTZ00121
Location:476 → 1099

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam11029
Location:146 → 214

DAZAP2; DAZ associated protein 2 (DAZAP2)

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2270 → 2448

Nipped-B_C; Sister chromatid cohesion C-terminus