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

Gene ID: 25836, updated on 2-Oct-2018

Summary

Official Symbol
NIPBLprovided by HGNC
Official Full Name
NIPBL, cohesin loading factorprovided by HGNC
Primary source
HGNC:HGNC:28862
See related
Ensembl:ENSG00000164190 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 cognitive disability. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 7.3), bone marrow (RPKM 7.1) and 25 other tissues See more
Orthologs

Genomic context

See NIPBL in Genome Data Viewer
Location:
5p13.2
Exon count:
48
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 divergent transcript Neighboring gene keratin 18 pseudogene 31 Neighboring gene ciliogenesis and planar polarity effector 1 Neighboring gene ribosomal protein S4X pseudogene 6 Neighboring gene chromosome 8 open reading frame 59 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
cohesin loading IDA
Inferred from Direct Assay
more info
PubMed 
developmental growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-strand break repair IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
establishment of mitotic sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
establishment of protein localization to chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heart morphogenesis IBA
Inferred from Biological aspect of Ancestor
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 chromosome condensation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitotic sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitotic sister chromatid cohesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II 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 mitotic cohesin loading IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ossification IEA
Inferred from Electronic Annotation
more info
 
rDNA condensation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
replication-born double-strand break repair via sister chromatid exchange IBA
Inferred from Biological aspect of Ancestor
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
 
transcriptional activation by promoter-enhancer looping IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
Scc2-Scc4 cohesin loading complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Scc2-Scc4 cohesin loading complex IDA
Inferred from Direct Assay
more info
PubMed 
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular exosome HDA PubMed 
integrator complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nipped-B-like protein
Names
Nipped-B homolog
SCC2 homolog
delangin
sister chromatid cohesion 2 homolog

NCBI Reference Sequences (RefSeq)

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
    ENSP00000406266.2, OTTHUMP00000221091, ENST00000448238.2, OTTHUMT00000366904
    Conserved Domains (5) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam08648
    Location:11031160
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:17941835
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22762454
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:18111839
    HEAT; HEAT repeat [structural motif]
  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
    ENSP00000282516.8, OTTHUMP00000116005, ENST00000282516.12, OTTHUMT00000207582
    Conserved Domains (5) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam08648
    Location:11031160
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:17941835
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22762454
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:18111839
    HEAT; HEAT repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006714467.2XP_006714530.1  nipped-B-like protein isoform X1

    Conserved Domains (5) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam08648
    Location:11031160
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:17941835
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22762418
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:18111839
    HEAT; HEAT repeat [structural motif]
  2. XM_005248280.3XP_005248337.1  nipped-B-like protein isoform X3

    See identical proteins and their annotated locations for XP_005248337.1

    Conserved Domains (5) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam08648
    Location:11031160
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:17941835
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22762454
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:18111839
    HEAT; HEAT repeat [structural motif]
  3. XM_006714468.2XP_006714531.1  nipped-B-like protein isoform X2

    Conserved Domains (4) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam12765
    Location:17281769
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22102388
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:17451773
    HEAT; HEAT repeat [structural motif]
  4. XM_017009331.1XP_016864820.1  nipped-B-like protein isoform X8

  5. XM_017009329.1XP_016864818.1  nipped-B-like protein isoform X4

  6. XM_011514015.1XP_011512317.1  nipped-B-like protein isoform X6

    Conserved Domains (5) summary
    pfam07223
    Location:113307
    DUF1421; Protein of unknown function (DUF1421)
    pfam08648
    Location:11031160
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:17941835
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:22762418
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:18111839
    HEAT; HEAT repeat [structural motif]
  7. XM_005248282.5XP_005248339.3  nipped-B-like protein isoform X5

  8. XM_017009330.2XP_016864819.1  nipped-B-like protein isoform X7

    UniProtKB/Swiss-Prot
    Q6KC79
    Conserved Domains (4) summary
    pfam08648
    Location:564621
    DUF1777; Protein of unknown function (DUF1777)
    pfam12765
    Location:12551296
    Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
    pfam12830
    Location:17371915
    Nipped-B_C; Sister chromatid cohesion C-terminus
    sd00044
    Location:12721300
    HEAT; HEAT repeat [structural motif]
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