Aliases for RUNDC3B Gene

Aliases for RUNDC3B Gene

  • RUN Domain Containing 3B 2 3 5
  • RPIB9 2 3 4
  • RPIP9 2 3 4
  • RUN Domain-Containing Protein 3B 3 4
  • Rap2-Interacting Protein 9 3 4
  • Rap2-Binding Protein 9 3 4
  • RPIP-9 3 4
  • Rap2 Binding Protein 9 3
  • RUNDC3B 5

External Ids for RUNDC3B Gene

Previous GeneCards Identifiers for RUNDC3B Gene

  • GC07P087096
  • GC07P087256
  • GC07P081867

Summaries for RUNDC3B Gene

GeneCards Summary for RUNDC3B Gene

RUNDC3B (RUN Domain Containing 3B) is a Protein Coding gene. An important paralog of this gene is RUNDC3A.

Additional gene information for RUNDC3B Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RUNDC3B Gene

Genomics for RUNDC3B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RUNDC3B Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J087627 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.9 852 3.2 SP1 ZNF692 BACH1 TARDBP FOXA1 LARP7 ZNF143 ZSCAN4 RBFOX2 POLR2A RUNDC3B DMTF1 SLC25A40 ABCB1 RF00994-1013 lnc-ABCB1-2
GH07J087873 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10.7 +249.3 249304 6.5 SP1 CREB1 GATAD2A HNRNPL PRDM10 ZNF629 REST ZNF512 RFX1 LEF1 DBF4 SLC25A40 lnc-ABCB1-3 piR-59233 RUNDC3B ABCB4 ADAM22
GH07J087574 Enhancer 1.2 FANTOM5 Ensembl ENCODE 17.2 -52.6 -52647 1 CREB1 ATF7 ZNF629 ZNF692 JUND PRDM1 PKNOX1 CEBPA SCRT2 CEBPB RUNDC3B SNODB1111 piR-37663-055 ABCB4 lnc-RUNDC3B-1 ABCB1
GH07J087598 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 12 -27.6 -27649 3.2 HNRNPL GATAD2A PRDM10 REST TFE3 NFKBIZ RCOR2 BACH1 PRDM1 RBFOX2 ABCB1 RUNDC3B SLC25A40 SNODB1111 piR-37663-055 lnc-ABCB1-2 ABCB4
GH07J087570 Enhancer 0.6 Ensembl ENCODE 16.9 -57.0 -57048 0.6 CEBPB FOS MAFK JUND RUNDC3B piR-37663-055 SNODB1111 ABCB4 lnc-RUNDC3B-1 ABCB1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RUNDC3B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RUNDC3B

Top Transcription factor binding sites by QIAGEN in the RUNDC3B gene promoter:
  • AREB6
  • E47
  • Egr-4
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • RSRFC4
  • Sp1

Genomic Locations for RUNDC3B Gene

Genomic Locations for RUNDC3B Gene
204,749 bases
Plus strand
204,750 bases
Plus strand

Genomic View for RUNDC3B Gene

Genes around RUNDC3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUNDC3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUNDC3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RUNDC3B Gene

Proteins for RUNDC3B Gene

  • Protein details for RUNDC3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RUN domain-containing protein 3B
    Protein Accession:
    Secondary Accessions:
    • B4DFD0
    • E9PBR4
    • Q8IWW5
    • Q8NB55
    • Q8TBG7

    Protein attributes for RUNDC3B Gene

    473 amino acids
    Molecular mass:
    52813 Da
    Quaternary structure:
    • Interacts with RAP2A.
    • Sequence=AAH22520.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for RUNDC3B Gene


neXtProt entry for RUNDC3B Gene

Post-translational modifications for RUNDC3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RUNDC3B Gene

Domains & Families for RUNDC3B Gene

Gene Families for RUNDC3B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RUNDC3B Gene


Suggested Antigen Peptide Sequences for RUNDC3B Gene

GenScript: Design optimal peptide antigens:
  • Rap2-interacting protein 9 (RUN3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the RUNDC3 family.
  • Belongs to the RUNDC3 family.
genes like me logo Genes that share domains with RUNDC3B: view

Function for RUNDC3B Gene

Phenotypes From GWAS Catalog for RUNDC3B Gene

genes like me logo Genes that share phenotypes with RUNDC3B: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RUNDC3B

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RUNDC3B Gene

Localization for RUNDC3B Gene

Subcellular locations from

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 RUNDC3B gene
Compartment Confidence
plasma membrane 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for RUNDC3B Gene

Pathways & Interactions for RUNDC3B Gene

PathCards logo

SuperPathways for RUNDC3B Gene

No Data Available

Gene Ontology (GO) - Biological Process for RUNDC3B Gene


No data available for Pathways by source and SIGNOR curated interactions for RUNDC3B Gene

Drugs & Compounds for RUNDC3B Gene

No Compound Related Data Available

Transcripts for RUNDC3B Gene

mRNA/cDNA for RUNDC3B Gene

7 NCBI additional mRNA sequence :
9 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 RUNDC3B

Alternative Splicing Database (ASD) splice patterns (SP) for RUNDC3B Gene

No ASD Table

Relevant External Links for RUNDC3B Gene

GeneLoc Exon Structure for

Expression for RUNDC3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RUNDC3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RUNDC3B Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.4).

Protein differential expression in normal tissues from HIPED for RUNDC3B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (53.9) and Heart (14.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RUNDC3B Gene

Protein tissue co-expression partners for RUNDC3B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RUNDC3B

SOURCE GeneReport for Unigene cluster for RUNDC3B Gene:


mRNA Expression by UniProt/SwissProt for RUNDC3B Gene:

Tissue specificity: Isoform 2 is expressed at high levels in brain, thymus, ovary, testis, leukocyte, liver, small intestine and prostate. Isoform 1 is expressed in the brain, testis and adrenal gland. It is activated in tumorigenic breast cancer cell lines and in the primary tumor of breast cancer patients. Activation also correlates with metastatic lymph node invasion and can be detected in metastatic epithelial cells from the lymph nodes and in the bone marrow of patients.

Evidence on tissue expression from TISSUES for RUNDC3B Gene

  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with RUNDC3B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RUNDC3B Gene

Orthologs for RUNDC3B Gene

This gene was present in the common ancestor of animals.

Orthologs for RUNDC3B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RUNDC3B 30 31
  • 99.79 (n)
(Canis familiaris)
Mammalia RUNDC3B 30 31
  • 94.68 (n)
(Bos Taurus)
Mammalia RUNDC3B 30 31
  • 92.74 (n)
(Mus musculus)
Mammalia Rundc3b 30 17 31
  • 88.83 (n)
(Rattus norvegicus)
Mammalia Rundc3b 30
  • 88.22 (n)
(Monodelphis domestica)
Mammalia RUNDC3B 31
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia RUNDC3B 31
  • 84 (a)
(Gallus gallus)
Aves RUNDC3B 30 31
  • 83.11 (n)
(Anolis carolinensis)
Reptilia RUNDC3B 31
  • 87 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia MGC76082 30
(Danio rerio)
Actinopterygii rundc3b 31
  • 76 (a)
Dr.28461 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG31064 31
  • 10 (a)
Species where no ortholog for RUNDC3B 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 Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for RUNDC3B Gene

Gene Tree for RUNDC3B (if available)
Gene Tree for RUNDC3B (if available)
Evolutionary constrained regions (ECRs) for RUNDC3B: view image

Paralogs for RUNDC3B Gene

(1) SIMAP similar genes for RUNDC3B Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with RUNDC3B: view

Variants for RUNDC3B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RUNDC3B Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
828497 Drug Response: Tramadol response 87,713,465(+) C/T INTRON_VARIANT
828498 Drug Response: Tramadol response 87,713,094(+) A/C INTRON_VARIANT
828499 Drug Response: Tramadol response 87,713,083(+) A/T INTRON_VARIANT
828500 Drug Response: Tramadol response 87,713,082(+) A/T INTRON_VARIANT
828501 Drug Response: Tramadol response 87,713,081(+) A/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for RUNDC3B Gene

Structural Variations from Database of Genomic Variants (DGV) for RUNDC3B Gene

Variant ID Type Subtype PubMed ID
dgv11489n54 CNV loss 21841781
esv2666273 CNV deletion 23128226
esv2734776 CNV deletion 23290073
esv28195 CNV loss 19812545
esv3542043 CNV deletion 23714750
esv3571956 CNV loss 25503493
esv3614037 CNV loss 21293372
esv7655 CNV loss 19470904
nsv464622 CNV gain 19166990
nsv477542 CNV novel sequence insertion 20440878
nsv528078 CNV loss 19592680
nsv607725 CNV gain 21841781
nsv607728 CNV loss 21841781

Variation tolerance for RUNDC3B Gene

Residual Variation Intolerance Score: 19.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.15; 23.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RUNDC3B Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RUNDC3B Gene

Disorders for RUNDC3B Gene

Additional Disease Information for RUNDC3B

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

No disorders were found for RUNDC3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RUNDC3B Gene

Publications for RUNDC3B Gene

  1. Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9). (PMID: 12645870) Wang S … Mao YM (Biochemical genetics 2003) 2 3 4 23
  2. Expression of RPIP9 (Rap2 interacting protein 9) is activated in breast carcinoma and correlates with a poor prognosis. (PMID: 15986426) Raguz S … Yagüe E (International journal of cancer 2005) 3 4 23
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4

Products for RUNDC3B Gene

Sources for RUNDC3B Gene