Aliases for RANBP3L Gene

Aliases for RANBP3L Gene

  • RAN Binding Protein 3 Like 2 3 5
  • Ran-Binding Protein 3-Like 3 4
  • RAN Binding Protein 3-Like 2
  • FLJ25422 2
  • RANBP3L 5

External Ids for RANBP3L Gene

Summaries for RANBP3L Gene

GeneCards Summary for RANBP3L Gene

RANBP3L (RAN Binding Protein 3 Like) is a Protein Coding gene. An important paralog of this gene is RANBP3.

UniProtKB/Swiss-Prot Summary for RANBP3L Gene

  • Nuclear export factor for BMP-specific SMAD1/5/8 that plays a critical role in terminating BMP signaling and regulating mesenchymal stem cell differentiation by blocking osteoblast differentiation to promote myogenic differention. Directly recognizes dephosphorylated SMAD1/5/8 and mediates their nuclear export in a Ran-dependent manner.

Additional gene information for RANBP3L Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RANBP3L Gene

Genomics for RANBP3L Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RANBP3L Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J036300 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 603.5 +0.6 628 2.6 CREB1 ATF7 PRDM10 REST ZNF629 ZNF692 FOXA1 PRDM1 SP1 ZNF501 RANBP3L NIPBL RNU6-1305P NADK2 SLC1A3 piR-47211-550
GH05J036238 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 19.5 +60.7 60658 5.1 RNF2 SP1 CREB1 GATAD2A CTCF HNRNPL PRDM10 REST ZNF629 TFE3 NADK2 NIPBL OFD1P17 RANBP3L NADK2-AS1 SLC1A3 SKP2
GH05J036688 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.9 -388.0 -388000 2.2 RNF2 CTCF TEAD4 PRDM10 ZNF629 KDM1A ZNF692 BACH1 LARP7 STAT3 WDR70 NIPBL NUP155 ENSG00000250155 SLC1A3 CPLANE1 RANBP3L NADK2-AS1 LOC107986413 piR-35674-411
GH05J036691 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 10.9 -390.3 -390279 2 CTCF LARP7 ZNF143 REST RAD21 ZNF501 TRIM22 EZH2 TCF7 CEBPB ENSG00000250155 SLC1A3 NADK2 RANBP3L NIPBL piR-35674-411 LOC107986413
GH05J036227 Enhancer 0.8 Ensembl ENCODE 18.4 +74.2 74213 1.8 GATAD2A ZNF7 PRDM1 RXRB CEBPA SOX13 FOXA2 RXRA GATA3 SOX5 RANBP3L NADK2 NADK2-AS1 SKP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RANBP3L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RANBP3L

Top Transcription factor binding sites by QIAGEN in the RANBP3L gene promoter:
  • c-Myc
  • FOXO4
  • GATA-1
  • HOXA9
  • HOXA9B
  • ITF-2
  • Max1
  • MRF-2
  • Olf-1
  • Tal-1beta

Genomic Locations for RANBP3L Gene

Genomic Locations for RANBP3L Gene
chr5:36,246,913-36,302,114
(GRCh38/hg38)
Size:
55,202 bases
Orientation:
Minus strand
chr5:36,248,536-36,302,216
(GRCh37/hg19)
Size:
53,681 bases
Orientation:
Minus strand

Genomic View for RANBP3L Gene

Genes around RANBP3L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RANBP3L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RANBP3L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RANBP3L Gene

Proteins for RANBP3L Gene

  • Protein details for RANBP3L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86VV4-RNB3L_HUMAN
    Recommended name:
    Ran-binding protein 3-like
    Protein Accession:
    Q86VV4
    Secondary Accessions:
    • B7Z866
    • E9PGP9
    • Q96LK2

    Protein attributes for RANBP3L Gene

    Size:
    465 amino acids
    Molecular mass:
    52211 Da
    Quaternary structure:
    • Interacts with SMAD1, SMAD5 and SMAD8; the interaction (with SMAD at least) increases when SMAD1 is not phosphorylated and mediates SMAD1 nuclear export.

    Alternative splice isoforms for RANBP3L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RANBP3L Gene

Post-translational modifications for RANBP3L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RANBP3L Gene

Domains & Families for RANBP3L Gene

Gene Families for RANBP3L Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RANBP3L Gene

InterPro:
Blocks:
  • RanBP1 domain
ProtoNet:

Suggested Antigen Peptide Sequences for RANBP3L Gene

GenScript: Design optimal peptide antigens:
  • Ran-binding protein 3-like (RNB3L_HUMAN)
genes like me logo Genes that share domains with RANBP3L: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RANBP3L Gene

Function for RANBP3L Gene

Molecular function for RANBP3L Gene

UniProtKB/Swiss-Prot Function:
Nuclear export factor for BMP-specific SMAD1/5/8 that plays a critical role in terminating BMP signaling and regulating mesenchymal stem cell differentiation by blocking osteoblast differentiation to promote myogenic differention. Directly recognizes dephosphorylated SMAD1/5/8 and mediates their nuclear export in a Ran-dependent manner.

Phenotypes From GWAS Catalog for RANBP3L Gene

Gene Ontology (GO) - Molecular Function for RANBP3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 contributes_to GTPase activator activity IBA 21873635
GO:0008536 Ran GTPase binding IBA 21873635
GO:0046332 SMAD binding IPI 25755279
genes like me logo Genes that share ontologies with RANBP3L: view
genes like me logo Genes that share phenotypes with RANBP3L: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RANBP3L

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RANBP3L Gene

Localization for RANBP3L Gene

Subcellular locations from UniProtKB/Swiss-Prot for RANBP3L Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RANBP3L gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RANBP3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005643 nuclear pore IBA 21873635
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with RANBP3L: view

Pathways & Interactions for RANBP3L Gene

PathCards logo

SuperPathways for RANBP3L Gene

No Data Available

Interacting Proteins for RANBP3L Gene

Gene Ontology (GO) - Biological Process for RANBP3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006611 protein export from nucleus IBA 21873635
GO:0043547 positive regulation of GTPase activity IEA --
GO:0045663 positive regulation of myoblast differentiation ISS --
GO:0045668 negative regulation of osteoblast differentiation ISS --
GO:0046907 intracellular transport IEA --
genes like me logo Genes that share ontologies with RANBP3L: view

No data available for Pathways by source and SIGNOR curated interactions for RANBP3L Gene

Drugs & Compounds for RANBP3L Gene

No Compound Related Data Available

Transcripts for RANBP3L Gene

mRNA/cDNA for RANBP3L Gene

10 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RANBP3L

Alternative Splicing Database (ASD) splice patterns (SP) for RANBP3L Gene

No ASD Table

Relevant External Links for RANBP3L Gene

GeneLoc Exon Structure for
RANBP3L

Expression for RANBP3L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RANBP3L Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RANBP3L Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.0), Brain - Caudate (basal ganglia) (x4.9), Brain - Amygdala (x4.9), and Brain - Putamen (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for RANBP3L Gene

This gene is overexpressed in Bone (58.2) and Stomach (10.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RANBP3L Gene



Protein tissue co-expression partners for RANBP3L Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RANBP3L

SOURCE GeneReport for Unigene cluster for RANBP3L Gene:

Hs.729817

Evidence on tissue expression from TISSUES for RANBP3L Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with RANBP3L: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RANBP3L Gene

Orthologs for RANBP3L Gene

This gene was present in the common ancestor of animals.

Orthologs for RANBP3L Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RANBP3L 30 31
  • 99.52 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RANBP3L 30 31
  • 87.62 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RANBP3L 30 31
  • 85.02 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ranbp3l 30 17 31
  • 78.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ranbp3l 30
  • 76.8 (n)
Oppossum
(Monodelphis domestica)
Mammalia RANBP3L 31
  • 53 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RANBP3L 31
  • 50 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RANBP3L 30 31
  • 66.26 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RANBP3L 31
  • 44 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ranbp3l 30
  • 50.07 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta RanBP3 31
  • 20 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ran-5 31
  • 18 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2235 31
  • 21 (a)
ManyToMany
-- 31
  • 15 (a)
ManyToMany
Species where no ortholog for RANBP3L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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 Vase (Ciona intestinalis)
  • 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)
  • Zebrafish (Danio rerio)

Evolution for RANBP3L Gene

ENSEMBL:
Gene Tree for RANBP3L (if available)
TreeFam:
Gene Tree for RANBP3L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RANBP3L: view image

Paralogs for RANBP3L Gene

Paralogs for RANBP3L Gene

(1) SIMAP similar genes for RANBP3L Gene using alignment to 2 proteins:

  • RNB3L_HUMAN
  • D6RCM9_HUMAN
genes like me logo Genes that share paralogs with RANBP3L: view

Variants for RANBP3L Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RANBP3L Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs1035480 - p.Thr70Arg
rs16902872 - p.Ala271Val
rs35433829 - p.Ala111Asp

Additional dbSNP identifiers (rs#s) for RANBP3L Gene

Structural Variations from Database of Genomic Variants (DGV) for RANBP3L Gene

Variant ID Type Subtype PubMed ID
esv2730076 CNV deletion 23290073
esv2730077 CNV deletion 23290073
esv2762515 CNV loss 21179565
esv3575836 CNV gain 25503493
esv3604707 CNV gain 21293372
esv3604714 CNV gain 21293372
esv3604715 CNV loss 21293372
nsv1015638 CNV gain 25217958
nsv830262 CNV gain 17160897

Variation tolerance for RANBP3L Gene

Residual Variation Intolerance Score: 68.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.04; 75.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RANBP3L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RANBP3L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RANBP3L Gene

Disorders for RANBP3L Gene

Additional Disease Information for RANBP3L

No disorders were found for RANBP3L Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RANBP3L Gene

Publications for RANBP3L Gene

  1. Nuclear Export of Smads by RanBP3L Regulates Bone Morphogenetic Protein Signaling and Mesenchymal Stem Cell Differentiation. (PMID: 25755279) Chen F … Feng XH (Molecular and cellular biology 2015) 2 3 4
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. Genetic variants in 5p13.2 and 7q21.1 are associated with treatment for benign prostatic hyperplasia with the α-adrenergic receptor antagonist. (PMID: 28787260) Qian X … Qi J (The aging male : the official journal of the International Society for the Study of the Aging Male 2017) 3

Products for RANBP3L Gene

Sources for RANBP3L Gene