RANBP9 RAN binding protein 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RANBP9provided by HGNC
Official Full Name: RAN binding protein 9provided by HGNC
Primary source: HGNC:HGNC:13727
See related: Ensembl:ENSG00000010017 MIM:603854; AllianceGenome:HGNC:13727
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: BPM-L; BPM90; RANBPM; RanBP7
Summary: This gene encodes a protein that binds RAN, a small GTP binding protein belonging to the RAS superfamily that is essential for the translocation of RNA and proteins through the nuclear pore complex. The protein encoded by this gene has also been shown to interact with several other proteins, including met proto-oncogene, homeodomain interacting protein kinase 2, androgen receptor, and cyclin-dependent kinase 11. [provided by RefSeq, Jul 2008]
Expression: Broad expression in testis (RPKM 72.2), esophagus (RPKM 38.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p23

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (13621498..13711835, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (13495055..13585361, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (13621730..13712067, complement)

Chromosome 6 - NC_000006.12 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: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ATM-Mediated translocation of RanBPM regulates DNA damage response by stabilizing p21 in non-small cell lung cancer cells.
Title: ATM-Mediated translocation of RanBPM regulates DNA damage response by stabilizing p21 in non-small cell lung cancer cells.
the present study provides preclinical and clinical data indicating that lower RANBP9 protein levels might be used, after perspective validation, as a biomarker predictive of response of non-small cell lung cancer to platinum based compounds
Title: RANBP9 affects cancer cells response to genotoxic stress and its overexpression is associated with worse response to platinum in NSCLC patients.
review provides a complete guide on RanBPM interactors, the physiological role of RanBPM in cellular functions, and potential applications in disease therapeutics.
Title: Scaffolding protein RanBPM and its interactions in diverse signaling pathways in health and disease.
Ran binding protein 9(RanBPM) is a scaffolding protein with a modulatory function that regulates the activities of IFN-stimulated response elements. IFN-lambda1 affects the cellular distribution of RanBPM and stimulates the interaction between RanBPM and interferon, lambda receptor 1(IFN-lambdaR1). Therefore, RanBPM plays a novel role in the IFN-lambda-regulated signaling pathway.
Title: Ran binding protein 9 (RanBPM) binds IFN-λR1 in the IFN-λ signaling pathway.
Our work shows that RanBPM, together with the CTLH complex, associates with HDAC6 and restricts cell migration through inhibition of HDAC6 activity. This study uncovers a novel function for the CTLH complex and suggests that it could have a tumour suppressive role in restricting HDAC6 oncogenic properties.
Title: Inhibition of HDAC6 activity through interaction with RanBPM and its associated CTLH complex.
High RANBPM expression is associated with cancer.
Title: Ubiquitin-specific protease 11 functions as a tumor suppressor by modulating Mgl-1 protein to regulate cancer cell growth.
RanBP9/TSSC3 complex cooperatively suppress metastasis via downregulation of Src-dependent Akt pathway to expedite mitochondrial-associated anoikis.
Title: RanBP9/TSSC3 complex cooperates to suppress anoikis resistance and metastasis via inhibiting Src-mediated Akt signaling in osteosarcoma.
Results show that increased expression of RanBPM associates with postponed disease progression and better prognosis suggesting that RanBPM plays an inhibitory role in regulating proliferation and invasion of lung cancer cells.
Title: Reduced Expression of RanBPM Is Associated with Poorer Survival from Lung Cancer and Increased Proliferation and Invasion of Lung Cancer Cells In Vitro.
The 20-mer peptide (residues 228-247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to a unique shallow binding surface on RanBPM formed by highly conserved loops on the surface of the beta-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface.
Title: Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.
RanBPM acts as a negative regulator of BLT2 and IL8, thus attenuating the invasiveness of aggressive breast cancer cells
Title: RanBPM inhibits BLT2-mediated IL-8 production and invasiveness in aggressive breast cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
integrase	gag-pol	Using acetylated HIV-1 IN as bait in yeast two-hybrid screening identifies nuclear import-export proteins Exp2 and RanBP9 as IN-binding partners	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L17993 (e-PCR)
- UniSTS:33026

SHGC-106866 (e-PCR)
- UniSTS:170064

SGC35035 (e-PCR)
- UniSTS:69270

AL020967 (e-PCR)
- UniSTS:68039

D6S1861 (e-PCR)
- UniSTS:17658

RH102430 (e-PCR)
- UniSTS:96764

D6S1430 (e-PCR)
- UniSTS:37374

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule nucleation	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of ERK1 and ERK2 cascade	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of positive regulation of amyloid precursor protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein-containing complex assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
part_of microtubule associated complex	TAS Traceable Author Statement more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ran-binding protein 9

Names: Ran Binding Protein in the Microtubule organizing center; novel centrosomal protein RanBPM; ran binding protein, centrosomal; ran-binding protein M

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_005493.3 → NP_005484.2 ran-binding protein 9

See identical proteins and their annotated locations for NP_005484.2

Status: REVIEWED

Source sequence(s)

AB055311, AF306510, BC052781, Z93020

Consensus CDS

CCDS4529.1

UniProtKB/Swiss-Prot

A0PJA2, B2R8E1, O94764, Q6P3T7, Q7LBR2, Q7Z7F9, Q96S59

Related

ENSP00000011619.3, ENST00000011619.6

Conserved Domains (4) summary

smart00667
Location:364 → 397

LisH; Lissencephaly type-1-like homology motif

smart00757
Location:616 → 708

CRA; CT11-RanBPM

cd12909
Location:189 → 331

SPRY_RanBP9_10; SPRY domain in Ran binding proteins 9 and 10

pfam10607
Location:403 → 457

CLTH; CTLH/CRA C-terminal to LisH motif domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

13621498..13711835 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514205.3 → XP_011512507.1 ran-binding protein 9 isoform X1

Conserved Domains (5) summary

smart00667
Location:364 → 397

LisH; Lissencephaly type-1-like homology motif

smart00668
Location:403 → 459

CTLH; C-terminal to LisH motif

smart00757
Location:526 → 618

CRA; CT11-RanBPM

pfam10607
Location:403 → 618

CLTH; CTLH/CRA C-terminal to LisH motif domain

cd12909
Location:189 → 331

SPRY_RanBP9_10; SPRY domain in Ran binding proteins 9 and 10
XM_047418032.1 → XP_047273988.1 ran-binding protein 9 isoform X3
XM_017010149.2 → XP_016865638.1 ran-binding protein 9 isoform X2