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RAP1B RAP1B, member of RAS oncogene family [ Homo sapiens (human) ]

Gene ID: 5908, updated on 5-Mar-2024

Summary

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Official Symbol
RAP1Bprovided by HGNC
Official Full Name
RAP1B, member of RAS oncogene familyprovided by HGNC
Primary source
HGNC:HGNC:9857
See related
Ensembl:ENSG00000127314 MIM:179530; AllianceGenome:HGNC:9857
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
K-REV; RAL1B; THC11
Summary
This gene encodes a member of the RAS-like small GTP-binding protein superfamily. Members of this family regulate multiple cellular processes including cell adhesion and growth and differentiation. This protein localizes to cellular membranes and has been shown to regulate integrin-mediated cell signaling. This protein also plays a role in regulating outside-in signaling in platelets. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 5, 6 and 9. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in lymph node (RPKM 83.8), appendix (RPKM 79.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q15
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (68610899..68671901)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (68590436..68651443)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (69004679..69065681)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene small integral membrane protein 3-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:68881905-68882736 Neighboring gene MPRA-validated peak1778 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr12:68932387-68933349 Neighboring gene ribosomal protein SA pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:69009467-69010238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6641 Neighboring gene ribosomal protein L10 pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6642 Neighboring gene small nucleolar RNA, H/ACA box 70G Neighboring gene MPRA-validated peak1779 silencer Neighboring gene ATP synthase peripheral stalk subunit d pseudogene 4 Neighboring gene uncharacterized LOC100507250 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:69074200-69074313 Neighboring gene ribosomal protein L7 pseudogene 42 Neighboring gene nucleoporin 107 Neighboring gene keratin 8 pseudogene 39

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. De novo missense variants in the RAP1B gene identified in two patients with syndromic thrombocytopenia. Niemann JH, et al. Clin Genet, 2020 Oct. PMID 32627184
  2. Long Noncoding RNA LUADT1 Is Upregulated in Melanoma and May Sponge miR-28-5p to Upregulate RAP1B. Xu JH, et al. Cancer Biother Radiopharm, 2020 May. PMID 32191497
  3. In Vitro Assay for the Rap GTPase-Activating Protein Activity of the Purified Cytoplasmic Domain of Plexin. Pascoe HG, et al. Methods Mol Biol, 2017. PMID 27787845
  4. Expression of RAP1B is associated with poor prognosis and promotes an aggressive phenotype in gastric cancer. Yang Y, et al. Oncol Rep, 2015 Nov. PMID 26329876
  5. β-Adrenergic receptors suppress Rap1B prenylation and promote the metastatic phenotype in breast cancer cells. Wilson JM, et al. Cancer Biol Ther, 2015. PMID 26209110, Free PMC Article

See all (146) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Adding to the evidence of gene-disease association of RAP1B and syndromic thrombocytopenia.
    Title: Adding to the evidence of gene-disease association of RAP1B and syndromic thrombocytopenia.
  2. ICP4-Associated Activation of Rap1b Facilitates Herpes Simplex Virus Type I (HSV-1) Infection in Human Corneal Epithelial Cells.
    Title: ICP4-Associated Activation of Rap1b Facilitates Herpes Simplex Virus Type I (HSV-1) Infection in Human Corneal Epithelial Cells.
  3. Roles of the hsa_circ_0013880/USP32/Rap1b axis in the proliferation and apoptosis of acute myeloid leukemia cells.
    Title: Roles of the hsa_circ_0013880/USP32/Rap1b axis in the proliferation and apoptosis of acute myeloid leukemia cells.
  4. SNORA70E promotes the occurrence and development of ovarian cancer through pseudouridylation modification of RAP1B and alternative splicing of PARPBP.
    Title: SNORA70E promotes the occurrence and development of ovarian cancer through pseudouridylation modification of RAP1B and alternative splicing of PARPBP.
  5. LINC00665 Facilitates the Malignant Processes of Osteosarcoma by Increasing the RAP1B Expression via Sponging miR-708 and miR-142-5p.
    Title: LINC00665 Facilitates the Malignant Processes of Osteosarcoma by Increasing the RAP1B Expression via Sponging miR-708 and miR-142-5p.
  6. De novo missense variants in the RAP1B gene identified in two patients with syndromic thrombocytopenia.
    Title: De novo missense variants in the RAP1B gene identified in two patients with syndromic thrombocytopenia.
  7. MiR-181a Reduces Platelet Activation via the Inhibition of Endogenous RAP1B.
    Title: MiR-181a Reduces Platelet Activation via the Inhibition of Endogenous RAP1B.
  8. Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis.
    Title: Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis.
  9. MicroRNA-149 inhibits the progression of lung adenocarcinoma through targeting RAP1B and inactivating Wnt/beta-catenin pathway.
    Title: MicroRNA-149 inhibits the progression of lung adenocarcinoma through targeting RAP1B and inactivating Wnt/β-catenin pathway.
  10. Long Noncoding RNA LUADT1 Is Upregulated in Melanoma and May Sponge miR-28-5p to Upregulate RAP1B.
    Title: Long Noncoding RNA LUADT1 Is Upregulated in Melanoma and May Sponge miR-28-5p to Upregulate RAP1B.
Submit: New GeneRIF Correction See all GeneRIFs (51)

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

Associated conditions

Description Tests
Thrombocytopenia 11 with multiple congenital anomalies and dysmorphic facies
MedGen: CN375875 OMIM: 620654 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of RAP1B, member of RAS oncogene family (RAP1B) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Protein interactions

Protein Gene Interaction Pubs
capsid gag Prostaglandin E2-mediated HIV-1 inhibition requires the EPAC/RAP/RhoA signaling pathway by downregulation of HIV-1 CA production PubMed

Go to the HIV-1, Human Interaction Database

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

Homology

Clone Names

  • FLJ18601, DKFZp586H0723

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G protein activity IEA
Inferred from Electronic Annotation
more info
  
enables GDP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GDP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in Rap protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in Rap protein signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in calcium-ion regulated exocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to cAMP IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to cAMP IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in establishment of endothelial barrier IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in microvillus assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in modification of postsynaptic structure IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of calcium ion-dependent exocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of synaptic vesicle exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of integrin activation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cell junction assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of establishment of cell polarity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in azurophil granule membrane TAS
Traceable Author Statement
more info
  
located_in cell-cell junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
NOT located_in membrane raft IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ras-related protein Rap-1b
Names
GTP-binding protein smg p21B
RAS-related protein RAP1B
Ras family small GTP binding protein RAP1B
small GTP binding protein
NP_001010942.1
NP_001238846.1
NP_001238847.1
NP_001238850.1
NP_001238851.1
NP_056461.1

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)

  1. NM_001010942.3 → NP_001010942.1  ras-related protein Rap-1b isoform 1 precursor

    See identical proteins and their annotated locations for NP_001010942.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB062128, AC015550, AC090061, CX868584, DB448914
    Consensus CDS
    CCDS8984.1
    UniProtKB/Swiss-Prot
    A6NIZ1, B2R5Z2, B4DQI8, B4DW74, B4DW94, P09526, P61224, Q502X3, Q5TZR4, Q6DCA1, Q6LES0
    Related
    ENSP00000250559.9, ENST00000250559.14
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

  2. NM_001251917.2 → NP_001238846.1  ras-related protein Rap-1b isoform 2

    See identical proteins and their annotated locations for NP_001238846.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two in-frame exons in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC015550, AC090061, AJ420497, AK301401, CX868584, DB448914
    Consensus CDS
    CCDS58254.1
    UniProtKB/TrEMBL
    B7ZAY2
    Related
    ENSP00000444830.1, ENST00000539091.5
    Conserved Domains (1) summary
    cl38936
    Location:3 → 125
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  3. NM_001251918.2 → NP_001238847.1  ras-related protein Rap-1b isoform 2

    See identical proteins and their annotated locations for NP_001238847.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks two in-frame exons in the coding region, compared to variant 1. The resulting isoform (2) is shorter, compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC015550, AC090061, AJ420497, AK316447, CX868584, DB448914
    Consensus CDS
    CCDS58254.1
    UniProtKB/TrEMBL
    B7ZAY2
    Related
    ENSP00000399986.2, ENST00000450214.6
    Conserved Domains (1) summary
    cl38936
    Location:3 → 125
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  4. NM_001251921.2 → NP_001238850.1  ras-related protein Rap-1b isoform 3

    See identical proteins and their annotated locations for NP_001238850.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC015550, AC090061, AJ420497, AK298818, CX868584, DB448914
    Consensus CDS
    CCDS58253.1
    UniProtKB/Swiss-Prot
    A6NIZ1
    Related
    ENSP00000446318.1, ENST00000540209.5
    Conserved Domains (1) summary
    cl38936
    Location:3 → 148
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  5. NM_001251922.2 → NP_001238851.1  ras-related protein Rap-1b isoform 4

    See identical proteins and their annotated locations for NP_001238851.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC015550, AC090061, AJ420497, AK301428, CX868584, DB448914
    Consensus CDS
    CCDS58252.1
    UniProtKB/Swiss-Prot
    P61224
    Related
    ENSP00000440014.1, ENST00000542145.5
    Conserved Domains (1) summary
    smart00010
    Location:2 → 121
    small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily

  6. NM_015646.6 → NP_056461.1  ras-related protein Rap-1b isoform 1 precursor

    See identical proteins and their annotated locations for NP_056461.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC015550, AC090061, BC000176, CX868584, DB448914
    Consensus CDS
    CCDS8984.1
    UniProtKB/Swiss-Prot
    A6NIZ1, B2R5Z2, B4DQI8, B4DW74, B4DW94, P09526, P61224, Q502X3, Q5TZR4, Q6DCA1, Q6LES0
    Related
    ENSP00000377085.5, ENST00000393436.9
    Conserved Domains (1) summary
    cd04175
    Location:3 → 167
    Rap1; Rap1 family GTPase consists of Rap1a and Rap1b isoforms

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    68610899..68671901
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    68590436..68651443
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61224.1 GenPept UniProtKB/Swiss-Prot:P61224

Gene LinkOut

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