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Aliases for NIPBL Gene

Aliases for NIPBL Gene

  • NIPBL, Cohesin Loading Factor 2 3
  • Nipped-B Homolog (Drosophila) 2 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 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around NIPBL on UCSC Golden Path with GeneCards custom track

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

Proteomics data for NIPBL Gene at MOPED

Post-translational modifications for NIPBL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NIPBL Gene

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:0008022 protein C-terminus binding IPI 17577209
GO:0047485 protein N-terminus binding IPI 16802858
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

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: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:0000278 mitotic cell cycle TAS --
GO:0001656 metanephros development NAS 15146185
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

Drugs & Compounds for NIPBL Gene

No Compound Related Data Available

Transcripts for NIPBL Gene

Unigene Clusters for NIPBL Gene

Nipped-B homolog (Drosophila):
Representative Sequences:

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 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, MOPED, and MaxQB for NIPBL Gene



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

Protein tissue co-expression partners for NIPBL Gene

- Elite partner

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
cow
(Bos Taurus)
Mammalia NIPBL 35
  • 95.53 (n)
  • 97.61 (a)
NIPBL 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NIPBL 35
  • 96.08 (n)
  • 98.04 (a)
NIPBL 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nipbl 35
  • 92.63 (n)
  • 96.89 (a)
Nipbl 16
Nipbl 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NIPBL 35
  • 99.85 (n)
  • 99.89 (a)
NIPBL 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nipbl 35
  • 91.98 (n)
  • 96.14 (a)
oppossum
(Monodelphis domestica)
Mammalia NIPBL 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 85 (a)
OneToMany
-- 36
  • 92 (a)
OneToMany
chicken
(Gallus gallus)
Aves LOC427439 35
  • 84.36 (n)
  • 89.7 (a)
-- 36
  • 88 (a)
OneToMany
-- 36
  • 88 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia NIPBL 36
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nipbl 35
  • 78.77 (n)
  • 88.85 (a)
zebrafish
(Danio rerio)
Actinopterygii nipblb 35
  • 68.72 (n)
  • 76.02 (a)
NIPBL (2 of 3) 36
  • 65 (a)
OneToMany
nipbla 36
  • 82 (a)
OneToMany
nipblb 36
  • 66 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009290 35
  • 28.58 (n)
  • 7.86 (a)
fruit fly
(Drosophila melanogaster)
Insecta Nipped-B 35
  • 51.35 (n)
  • 43.53 (a)
Nipped-B 36
  • 35 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea pqn-85 36
  • 27 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCC2 36
  • 20 (a)
OneToOne
SCC2 38
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9744 36
  • 46 (a)
OneToOne
Species with no ortholog for NIPBL:
  • 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
rs3822471 -, - 36,985,201(+) ACAAA(A/G)TGAAA reference, missense
VAR_019519 Cornelia de Lange syndrome 1 (CDLS1)
VAR_019520 Cornelia de Lange syndrome 1 (CDLS1)
VAR_019521 Cornelia de Lange syndrome 1 (CDLS1)
VAR_021597 -

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

Variant ID Type Subtype PubMed ID
nsv525478 CNV Loss 19592680
nsv830264 CNV Loss 17160897
esv2525217 CNV Deletion 19546169
dgv6036n71 CNV Loss 21882294
nsv880502 CNV Loss 21882294

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

HapMap Linkage Disequilibrium report
NIPBL
Human Gene Mutation Database (HGMD)
NIPBL

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

Disorders for NIPBL Gene

MalaCards: The human disease database

(11) 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
  • amstelodamensis typus degenerativus
nipbl-related cornelia de lange syndrome
  • cornelia de lange syndrome 1
cornelia de lange syndrome
  • brachmann de lange syndrome
chromosome 5p13 duplication syndrome
  • 5p13 microduplication syndrome
developmental disabilities
- 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 23 48 67
  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 23
  3. Genomic duplication resulting in increased copy number of genes encoding the sister chromatid cohesion complex conveys clinical consequences distinct from Cornelia de Lange. (PMID: 19052029) Yan J. … Lupski J.R. (J. Med. Genet. 2009) 3 23
  4. Cornelia de Lange syndrome (CdLS): prenatal and autopsy findings. (PMID: 19242925) Chong K. … Chitayat D. (Prenat. Diagn. 2009) 3 23
  5. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. (PMID: 19468298) Liu J. … Krantz I.D. (PLoS Biol. 2009) 3 23

Products for NIPBL Gene

Sources for NIPBL Gene

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