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Aliases for NIPBL Gene

Aliases for NIPBL Gene

  • NIPBL, Cohesin Loading Factor 2 3 5
  • SCC2 Homolog 3 4
  • Delangin 3 4
  • IDN3 3 4
  • Sister Chromatid Cohesion 2 Homolog (Yeast) 2
  • Sister Chromatid Cohesion 2 Homolog 3
  • Nipped-B Homolog (Drosophila) 2
  • Nipped-B-Like Protein 3
  • Nipped-B Homolog 3
  • IDN3-B 3
  • CDLS1 3
  • CDLS 3
  • Scc2 3

External Ids for NIPBL Gene

Previous GeneCards Identifiers for NIPBL Gene

  • GC05P036912

Summaries for NIPBL Gene

Entrez Gene Summary for NIPBL Gene

  • 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 mental retardation. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for NIPBL Gene

NIPBL (NIPBL, Cohesin Loading Factor) is a Protein Coding gene. Diseases associated with NIPBL include Cornelia De Lange Syndrome 1 and Nipbl-Related Cornelia De Lange Syndrome. Among its related pathways are Cell Cycle, Mitotic and Mitotic Telophase/Cytokinesis. GO annotations related to this gene include chromatin binding and protein C-terminus binding.

UniProtKB/Swiss-Prot for NIPBL Gene

  • Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by interacting with the cohesin complex (By similarity).

Gene Wiki entry for NIPBL Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIPBL Gene

Genomics for NIPBL Gene

Regulatory Elements for NIPBL Gene

Enhancers for NIPBL Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F036898 1.3 FANTOM5 Ensembl 16 +21.7 21742 1.0 NIPBL KRT18P31 GC05P037069
GH05F036899 0.2 Ensembl 12.7 +22.9 22942 0.2 SUPT20H NIPBL KRT18P31 GC05P037069
GH05F036900 0.2 Ensembl 12.7 +23.6 23642 0.4 ESRRA NIPBL KRT18P31 GC05P037069
GH05F036904 0.2 Ensembl 12.7 +27.9 27942 1.0 CEBPA HLF CEBPB NIPBL KRT18P31 GC05P037069
GH05F036928 1 Ensembl ENCODE 12.3 +52.1 52146 0.6 PKNOX1 ZNF76 INSM2 FEZF1 GLI4 ZNF2 ZEB1 GLIS2 ZNF302 ZNF366 WDR70 C5orf42 ENSG00000250155 OFD1P17 NIPBL KRT18P31 GC05P037069
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around NIPBL on UCSC Golden Path with GeneCards custom track

Promoters for NIPBL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001278296 -58 6600 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for NIPBL Gene

Chromosome:
5
Start:
36,876,759 bp from pter
End:
37,066,413 bp from pter
Size:
189,655 bases
Orientation:
Plus strand

Genomic View for NIPBL Gene

Genes around NIPBL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPBL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPBL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPBL Gene

Proteins for NIPBL Gene

  • Protein details for NIPBL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6KC79-NIPBL_HUMAN
    Recommended name:
    Nipped-B-like protein
    Protein Accession:
    Q6KC79
    Secondary Accessions:
    • Q6KCD6
    • Q6N080
    • Q6ZT92
    • Q7Z2E6
    • Q8N4M5
    • Q9Y6Y3
    • Q9Y6Y4

    Protein attributes for NIPBL Gene

    Size:
    2804 amino acids
    Molecular mass:
    316051 Da
    Quaternary structure:
    • Interacts directly with CBX5 via the PxVxL motif. Interacts with SCC4 (via N-terminus) to form the cohesin loading complex (PubMed:16802858, PubMed:16682347, PubMed:21934712).
    SequenceCaution:
    • Sequence=AAH33847.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA77335.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA.; Evidence={ECO:0000305}; Sequence=BAA77349.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA.; Evidence={ECO:0000305}; Sequence=BAC86701.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAE45790.1; Type=Frameshift; Positions=278; Evidence={ECO:0000305};

    Alternative splice isoforms for NIPBL Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NIPBL Gene

Post-translational modifications for NIPBL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NIPBL Gene

Domains & Families for NIPBL Gene

Protein Domains for NIPBL Gene

Suggested Antigen Peptide Sequences for NIPBL Gene

Graphical View of Domain Structure for InterPro Entry

Q6KC79

UniProtKB/Swiss-Prot:

NIPBL_HUMAN :
  • Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain.
  • Belongs to the SCC2/Nipped-B family.
  • Contains 5 HEAT repeats.
Domain:
  • Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain.
Family:
  • Belongs to the SCC2/Nipped-B family.
Similarity:
  • Contains 5 HEAT repeats.
genes like me logo Genes that share domains with NIPBL: view

No data available for Gene Families for NIPBL Gene

Function for NIPBL Gene

Molecular function for NIPBL Gene

UniProtKB/Swiss-Prot Function:
Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by interacting with the cohesin complex (By similarity).

Gene Ontology (GO) - Molecular Function for NIPBL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 16682347
GO:0008022 protein C-terminus binding IPI 17577209
GO:0036033 mediator complex binding IEA --
GO:0042826 histone deacetylase binding IPI 18854353
genes like me logo Genes that share ontologies with NIPBL: view
genes like me logo Genes that share phenotypes with NIPBL: view

Human Phenotype Ontology for NIPBL Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NIPBL Gene

MGI Knock Outs for NIPBL:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for NIPBL Gene

Localization for NIPBL Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPBL Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NIPBL Gene COMPARTMENTS Subcellular localization image for NIPBL gene
Compartment Confidence
extracellular 5
nucleus 5
endoplasmic reticulum 2
plasma membrane 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for NIPBL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IEA --
GO:0005634 nucleus IEA,IDA 16802858
GO:0005654 nucleoplasm TAS --
GO:0032116 SMC loading complex IDA 16682347
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with NIPBL: view

Pathways & Interactions for NIPBL Gene

genes like me logo Genes that share pathways with NIPBL: view

Pathways by source for NIPBL Gene

Gene Ontology (GO) - Biological Process for NIPBL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 18854353
GO:0001656 metanephros development NAS 15146185
GO:0003007 heart morphogenesis IMP 8291537
GO:0003151 outflow tract morphogenesis IMP 19242925
GO:0006974 cellular response to DNA damage stimulus IMP 17468178
genes like me logo Genes that share ontologies with NIPBL: view

No data available for SIGNOR curated interactions for NIPBL Gene

Transcripts for NIPBL Gene

Unigene Clusters for NIPBL Gene

Nipped-B homolog (Drosophila):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIPBL Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

ExUns: 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40a · 40b ^ 41 ^ 42a · 42b ^ 43 ^ 44 ^ 45a · 45b · 45c ^ 46 ^
SP1: - -
SP2: - -
SP3:
SP4:
SP5: - -
SP6:
SP7: -
SP8:

ExUns: 47a · 47b · 47c ^ 48a · 48b
SP1: - -
SP2:
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8:

Relevant External Links for NIPBL Gene

GeneLoc Exon Structure for
NIPBL
ECgene alternative splicing isoforms for
NIPBL

Expression for NIPBL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NIPBL Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NIPBL Gene

This gene is overexpressed in Peripheral blood mononuclear cells (25.4) and Esophagus (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NIPBL Gene



Protein tissue co-expression partners for NIPBL Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NIPBL Gene:

NIPBL

SOURCE GeneReport for Unigene cluster for NIPBL Gene:

Hs.481927

mRNA Expression by UniProt/SwissProt for NIPBL Gene:

Q6KC79-NIPBL_HUMAN
Tissue specificity: Widely expressed. Highly expressed in heart, skeletal muscle, fetal and adult liver, fetal and adult kidney. Expressed at intermediates level in thymus, placenta, peripheral leukocyte and small intestine. Weakly or not expressed in brain, colon, spleen and lung.
genes like me logo Genes that share expression patterns with NIPBL: view

Primer Products

No data available for mRNA differential expression in normal tissues for NIPBL Gene

Orthologs for NIPBL Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NIPBL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NIPBL 34 35
  • 99.85 (n)
dog
(Canis familiaris)
Mammalia NIPBL 34 35
  • 96.08 (n)
cow
(Bos Taurus)
Mammalia NIPBL 34 35
  • 95.53 (n)
mouse
(Mus musculus)
Mammalia Nipbl 34 16 35
  • 92.63 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 92 (a)
OneToMany
-- 35
  • 85 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Nipbl 34
  • 91.98 (n)
oppossum
(Monodelphis domestica)
Mammalia NIPBL 35
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 35
  • 88 (a)
OneToMany
-- 35
  • 88 (a)
OneToMany
LOC427439 34
  • 84.36 (n)
lizard
(Anolis carolinensis)
Reptilia NIPBL 35
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nipbl 34
  • 78.77 (n)
zebrafish
(Danio rerio)
Actinopterygii nipbla 35
  • 82 (a)
OneToMany
nipblb 34 35
  • 68.72 (n)
NIPBL (2 of 3) 35
  • 65 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Nipped-B 34 35
  • 51.35 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009290 34
  • 28.58 (n)
worm
(Caenorhabditis elegans)
Secernentea pqn-85 35
  • 27 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCC2 35 37
  • 20 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9744 35
  • 46 (a)
OneToOne
Species where no ortholog for NIPBL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NIPBL Gene

ENSEMBL:
Gene Tree for NIPBL (if available)
TreeFam:
Gene Tree for NIPBL (if available)

Paralogs for NIPBL Gene

No data available for Paralogs for NIPBL Gene

Variants for NIPBL Gene

Sequence variations from dbSNP and Humsavar for NIPBL Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs121918265 Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470], Pathogenic 37,057,211(+) CTTGT(A/G)TATAG intron-variant, reference, missense
rs121918268 Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470], Pathogenic 37,002,734(+) ATCTG(C/G)TAAAA reference, missense
rs142923613 Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470], other 36,962,199(+) CATAC(A/G)CCCCA reference, missense
rs149629686 Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470] 36,985,783(+) AGAAC(A/G)AAAAC intron-variant, reference, missense
rs587784024 Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470], Pathogenic 37,049,240(+) TGTAC(A/G)CCACT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NIPBL Gene

Variant ID Type Subtype PubMed ID
dgv5632n100 CNV loss 25217958
dgv5633n100 CNV loss 25217958
esv2525217 CNV deletion 19546169
esv3570072 CNV loss 25503493
esv3570073 CNV loss 25503493
esv3570074 CNV loss 25503493
nsv1033562 CNV loss 25217958
nsv1033928 CNV loss 25217958
nsv1161231 CNV deletion 26073780
nsv525478 CNV loss 19592680
nsv597822 CNV loss 21841781
nsv830264 CNV loss 17160897
nsv964843 CNV duplication 23825009

Variation tolerance for NIPBL Gene

Residual Variation Intolerance Score: 0.41% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.46; 71.57% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NIPBL Gene

Human Gene Mutation Database (HGMD)
NIPBL
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NIPBL

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIPBL Gene

Disorders for NIPBL Gene

MalaCards: The human disease database

(8) MalaCards diseases for NIPBL Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cornelia de lange syndrome 1
  • cornelia de lange syndrome
nipbl-related cornelia de lange syndrome
  • cornelia de lange syndrome 1
chromosome 5p13 duplication syndrome
  • 5p13 microduplication syndrome
obesity, hyperphagia, and developmental delay
  • obhd
sc phocomelia syndrome
  • hypomelia hypotrichosis facial hemangioma syndrome
- elite association - COSMIC cancer census association via MalaCards
Search NIPBL in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NIPBL_HUMAN
  • Cornelia de Lange syndrome 1 (CDLS1) [MIM:122470]: A form of Cornelia de Lange syndrome, a clinically heterogeneous developmental disorder associated with malformations affecting multiple systems. Characterized by facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal dysfunction and cardiac, ophthalmologic and genitourinary anomalies. {ECO:0000269 PubMed:15146185, ECO:0000269 PubMed:15146186, ECO:0000269 PubMed:15318302, ECO:0000269 PubMed:20124326, ECO:0000269 PubMed:20358602, ECO:0000269 PubMed:21934712, ECO:0000269 PubMed:23254390, ECO:0000269 PubMed:25447906}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NIPBL

Genetic Association Database (GAD)
NIPBL
Human Genome Epidemiology (HuGE) Navigator
NIPBL
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NIPBL
genes like me logo Genes that share disorders with NIPBL: view

No data available for Genatlas for NIPBL Gene

Publications for NIPBL Gene

  1. Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. (PMID: 20358602) Pie J. … Ramos F.J. (Am. J. Med. Genet. A 2010) 3 4 22 46 64
  2. Clinical and genetic analysis of Korean patients with Cornelia de Lange syndrome: two novel NIPBL mutations. (PMID: 20124326) Park H.D. … Kim J.K. (Ann. Clin. Lab. Sci. 2010) 3 4 22 64
  3. Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance. (PMID: 16802858) Seitan V.C. … Strachan T. (PLoS Biol. 2006) 3 4 22 64
  4. NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome. (PMID: 15146185) Tonkin E.T. … Strachan T. (Nat. Genet. 2004) 2 3 4 64
  5. Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. (PMID: 15146186) Krantz I.D. … Jackson L.G. (Nat. Genet. 2004) 2 3 4 64

Products for NIPBL Gene

Sources for NIPBL Gene

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