Nipbl NIPBL, cohesin loading factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nipblprovided by RGD
Official Full Name: NIPBL, cohesin loading factorprovided by RGD
Primary source: RGD:1306393
See related: EnsemblRapid:ENSRNOG00000056907 AllianceGenome:RGD:1306393
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: IDN3
Summary: Predicted to enable several functions, including chromo shadow domain binding activity; cohesin loader activity; and histone deacetylase binding activity. Predicted to be involved in several processes, including chromosome organization; embryonic morphogenesis; and reproductive structure development. Predicted to act upstream of or within several processes, including embryonic cranial skeleton morphogenesis; fat cell differentiation; and positive regulation of ossification. Predicted to be located in chromatin; cytosol; and nucleoplasm. Predicted to be part of Scc2-Scc4 cohesin loading complex and integrator complex. 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]
Expression: Biased expression in Thymus (RPKM 384.2), Spleen (RPKM 264.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q16

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (59126676..59314841, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (57399443..57586770, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (57508830..57676197, complement)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

AW532132 (e-PCR)
- UniSTS:245560

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

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

BE117972 (e-PCR)
- UniSTS:248737

RH143372 (e-PCR)
- UniSTS:232619

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

Omy1296INRA (e-PCR)
- UniSTS:512481

AU025529 (e-PCR)
- UniSTS:115173

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromo shadow domain binding	ISO Inferred from Sequence Orthology more info
enables cohesin loader activity	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables mediator complex binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in cellular response to X-ray	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in cognition	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic digestive tract morphogenesis	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in eye morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in face morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in gallbladder development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
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 mitotic sister chromatid cohesion	ISO Inferred from Sequence Orthology more info
involved_in mitotic sister chromatid segregation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of ossification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in regulation of hair cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology 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 sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	ISO Inferred from Sequence Orthology 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 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
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of integrator complex	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nipped-B-like protein

Names: Nipped-B homolog; delangin

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_001427697.1 → NP_001414626.1 nipped-B-like protein isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A0A8I6AXR8

Related

ENSRNOP00000071473.3, ENSRNOT00000083247.3
NM_001427698.1 → NP_001414627.1 nipped-B-like protein isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A0A8I5ZLR4, A0A8I6AXR8

Related

ENSRNOP00000078828.1, ENSRNOT00000097994.2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

59126676..59314841 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039103537.2 → XP_038959465.1 nipped-B-like protein isoform X1

UniProtKB/TrEMBL

A0A8I6AXR8

Conserved Domains (6) summary

PTZ00121
Location:559 → 1110

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2271 → 2447

Nipped-B_C; Sister chromatid cohesion C-terminus

cd19953
Location:1838 → 1872

PDS5; HEAT repeat [structural motif]

NF033839
Location:593 → 830

PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form
XM_063281521.1 → XP_063137591.1 nipped-B-like protein isoform X1

UniProtKB/TrEMBL

A0A8I6AXR8
XM_039103539.2 → XP_038959467.1 nipped-B-like protein isoform X2

UniProtKB/TrEMBL

A0A8I6AXR8

Conserved Domains (6) summary

PTZ00121
Location:559 → 1110

PTZ00121; MAEBL; Provisional

sd00044
Location:1805 → 1833

HEAT; HEAT repeat [structural motif]

pfam12765
Location:1788 → 1829

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2271 → 2447

Nipped-B_C; Sister chromatid cohesion C-terminus

cd19953
Location:1838 → 1872

PDS5; HEAT repeat [structural motif]

NF033839
Location:593 → 830

PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form
XM_039103540.2 → XP_038959468.1 nipped-B-like protein isoform X3

UniProtKB/TrEMBL

A0A8I6AXR8

Conserved Domains (6) summary

PTZ00121
Location:448 → 999

PTZ00121; MAEBL; Provisional

sd00044
Location:1694 → 1722

HEAT; HEAT repeat [structural motif]

pfam12765
Location:1677 → 1718

Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion

pfam12830
Location:2160 → 2336

Nipped-B_C; Sister chromatid cohesion C-terminus

cd19953
Location:1727 → 1761

PDS5; HEAT repeat [structural motif]

NF033839
Location:482 → 719

PspC_subgroup_2; pneumococcal surface protein PspC, LPXTG-anchored form

RNA

XR_010063589.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001106415.1: Suppressed sequence

Description

NM_001106415.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: NIPBL (GeneID:25836).