Nipped-B Nipped-B [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Nipped-Bprovided by FlyBase
Official Full Name: Nipped-Bprovided by FlyBase
Primary source: FLYBASE:FBgn0026401
Locus tag: Dmel_CG17704
See related: AllianceGenome:FB:FBgn0026401
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: CG17704; CG40281; Dmel\CG17704; l(2)02047; Nip-B; NipB; nipped-B; NIPPED-B
Summary: Enables chromatin binding activity and cohesin loader activity. Involved in several processes, including chromosome organization; learning or memory; and positive regulation of macromolecule biosynthetic process. Located in euchromatin; nucleus; and polytene chromosome. Is expressed in organism and spermatozoon. Used to study Cornelia de Lange syndrome. 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, Dec 2024]
Orthologs: all
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Genomic context

Location:: 41B3-41C1; 2-55 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	2R	NT_033778.4 (4691672..4729017, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	2R	NT_033778.3 (579177..616522, complement)

Chromosome 2R - NT_033778.4 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

studies confirm that Drosophila Nipped-B mutants provide a useful model for understanding CdLS, and provide new insights into the origins of birth defects
Title: Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior.
Nipped-B and Pds5 regulate transcription by controlling how much cohesin binds DNA in the stable mode, and not binding affinity.
Title: Dosage-sensitive regulation of cohesin chromosome binding and dynamics by Nipped-B, Pds5, and Wapl.
Nipped-B & cohesin co-localize on chromosomes, & bind actively transcribed genes & control regulatory sequences, like transcriptional enhancers & insulators. They may define active chromatin domains & influence transcriptional elongation. Review.
Title: Cohesin, gene expression and development: lessons from Drosophila.
Data show that Nipped-B is required for sister chromatid cohesion but that, opposite to the effect of Nipped-B, the stromalin/Scc3 component of Cohesin inhibits long-range activation of cut.
Title: Drosophila nipped-B protein supports sister chromatid cohesion and opposes the stromalin/Scc3 cohesion factor to facilitate long-range activation of the cut gene.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Dm0206 (e-PCR)
- UniSTS:79494

Homology

NCBI Orthologs

Orthologs from OrthoDB

mobile_element

Loc: c4694037-4693650 mobile_element_type = transposon:INE-1{}4314
Loc: c4696512-4695967 mobile_element_type = transposon:INE-1{}4316
Loc: c4700015-4699427 mobile_element_type = transposon:INE-1{}4319
Loc: c4700337-4700199 mobile_element_type = transposon:INE-1{}4328
Loc: c4701839-4701316 mobile_element_type = transposon:INE-1{}4329
Loc: c4703707-4703617 mobile_element_type = transposon:INE-1{}4331
Loc: c4706065-4705391 mobile_element_type = transposon:INE-1{}4337
Loc: c4706810-4706331 mobile_element_type = transposon:Fw2{}5201
Loc: c4706916-4706849 mobile_element_type = transposon:Fw3{}5206
Loc: c4709105-4708665 mobile_element_type = transposon:gypsy8{}5151
Loc: c4709293-4709106 mobile_element_type = transposon:1360{}4551
Loc: c4709655-4709618 mobile_element_type = transposon:INE-1{}4344
Loc: c4709793-4709656 mobile_element_type = transposon:accord2{}5198
Loc: c4710713-4710173 mobile_element_type = transposon:Tc1-2{}5044
Loc: c4711237-4710886 mobile_element_type = transposon:INE-1{}4346
Loc: c4714350-4714277 mobile_element_type = transposon:transib2{}5060
Loc: c4714923-4712838 mobile_element_type = transposon:Cr1a{}5009
Loc: c4715516-4715383 mobile_element_type = transposon:Tc3{}2828
Loc: c4716226-4715040 mobile_element_type = transposon:invader6{}5119
Loc: c4718980-4716903 mobile_element_type = transposon:INE-1{}2827
Loc: c4719501-4719433 mobile_element_type = transposon:INE-1{}2826
Loc: c4719661-4719608 mobile_element_type = transposon:INE-1{}4361
Loc: c4720472-4720355 mobile_element_type = transposon:INE-1{}4363
Loc: c4723076-4722925 mobile_element_type = transposon:INE-1{}4366
Loc: c4726494-4726295 mobile_element_type = transposon:INE-1{}4369

Gene Ontology Provided by FlyBase

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 chromatin binding	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	IGI Inferred from Genetic Interaction more info	PubMed
involved_in circadian sleep/wake cycle, sleep	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 learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of mitotic sister chromatid cohesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic sister chromatid cohesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in replication-born double-strand break repair via sister chromatid exchange	IBA Inferred from Biological aspect of Ancestor more info
involved_in short-term memory	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptonemal complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptonemal complex organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
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
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in polytene chromosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: Nipped-B

Names: CG17704-PE; CG17704-PF; CG17704-PG; CG17704-PH; CG17704-PI; CG17704-PJ; NipB; Nipped-B-PE; Nipped-B-PF; Nipped-B-PG; Nipped-B-PH; Nipped-B-PI; Nipped-B-PJ; NippedB; nipped; nipped B

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NT_033778.4 Reference assembly

Range

4691672..4729017 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001169581.2 → NP_001163052.1 Nipped-B, isoform G [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001163052.1

Status: REVIEWED

UniProtKB/TrEMBL

A8WHK9, E1JGX3

Conserved Domains (2) summary

pfam12765
Location:1127 → 1168

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1619 → 1802

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_001169583.2 → NP_001163054.1 Nipped-B, isoform I [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001163054.1

Status: REVIEWED

UniProtKB/TrEMBL

A8WHK9, E1JGX3

Conserved Domains (2) summary

pfam12765
Location:1127 → 1168

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1619 → 1802

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_001042986.3 → NP_001036451.1 Nipped-B, isoform F [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001036451.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4UZ37, Q058T3, Q058T4, Q7PLI2, Q7PLI3, Q9XYM2

UniProtKB/TrEMBL

A8WHK9

Conserved Domains (2) summary

pfam12765
Location:1151 → 1192

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1643 → 1826

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_001169582.2 → NP_001163053.1 Nipped-B, isoform H [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001163053.1

Status: REVIEWED

UniProtKB/TrEMBL

A8WHK9, E1JGX3

Conserved Domains (2) summary

pfam12765
Location:1127 → 1168

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1619 → 1802

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_001042987.3 → NP_001036452.1 Nipped-B, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001036452.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4UZ37, Q058T3, Q058T4, Q7PLI2, Q7PLI3, Q9XYM2

UniProtKB/TrEMBL

A8WHK9

Conserved Domains (2) summary

pfam12765
Location:1151 → 1192

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1643 → 1826

Nipped-B_C; Sister chromatid cohesion C-terminus
NM_001273774.1 → NP_001260703.1 Nipped-B, isoform J [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001260703.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4KF23, A8WHK9

Conserved Domains (2) summary

pfam12765
Location:1031 → 1072

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:1523 → 1706

Nipped-B_C; Sister chromatid cohesion C-terminus