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RAPGEF6 Rap guanine nucleotide exchange factor 6 [ Homo sapiens (human) ]

Gene ID: 51735, updated on 24-Nov-2020

Summary

Official Symbol
RAPGEF6provided by HGNC
Official Full Name
Rap guanine nucleotide exchange factor 6provided by HGNC
Primary source
HGNC:HGNC:20655
See related
Ensembl:ENSG00000158987 MIM:610499
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RAGEF2; PDZGEF2; KIA001LB; PDZ-GEF2; RA-GEF-2
Expression
Ubiquitous expression in lymph node (RPKM 9.8), appendix (RPKM 6.5) and 24 other tissues See more
Orthologs

Genomic context

See RAPGEF6 in Genome Data Viewer
Location:
5q31.1
Exon count:
31
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (131423921..131635229, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (130759614..130970929, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene LYR motif containing 7 Neighboring gene CDC42 small effector 2 Neighboring gene uncharacterized LOC105379173 Neighboring gene folliculin interacting protein 1 Neighboring gene ACTB pseudogene 4 Neighboring gene meiotic kinetochore factor

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of Rap guanine nucleotide exchange factor (GEF) 6 (RAPGEF6) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: FNIP1

Homology

Clone Names

  • DKFZp667N084, DKFZp686I15116

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTP-dependent protein binding IDA
Inferred from Direct Assay
more info
PubMed 
guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
small GTPase binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Ras protein signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
NOT establishment of endothelial intestinal barrier IMP
Inferred from Mutant Phenotype
more info
PubMed 
microvillus assembly IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of GTPase activity NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
endocytic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
rap guanine nucleotide exchange factor 6
Names
PDZ domain containing guanine nucleotide exchange factor (GEF) 2
PDZ domain-containing guanine nucleotide exchange factor 2
PDZ domain-containing guanine nucleotide exchange factor I
Rap guanine nucleotide exchange factor (GEF) 6

NCBI Reference Sequences (RefSeq)

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_001164386.2NP_001157858.1  rap guanine nucleotide exchange factor 6 isoform 1

    See identical proteins and their annotated locations for NP_001157858.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF478567, AL832899, AV726501, BC140820, DA817493
    Consensus CDS
    CCDS54900.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    UniProtKB/TrEMBL
    B2RTU6
    Related
    ENSP00000296859.6, ENST00000296859.10
    Conserved Domains (7) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    COG0664
    Location:274448
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:8571081
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:749833
    UBQ; Ubiquitin-like proteins
  2. NM_001164387.2NP_001157859.1  rap guanine nucleotide exchange factor 6 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) includes an alternate in-frame exon in the central coding region but lacks another alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.
    Source sequence(s)
    AF394782, AF478567, AL832899, AV726501, BU568060, DA817493
    Consensus CDS
    CCDS54901.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    Related
    ENSP00000426081.2, ENST00000507093.5
    Conserved Domains (7) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    COG0664
    Location:274448
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:8621086
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:754838
    UBQ; Ubiquitin-like proteins
  3. NM_001164388.2NP_001157860.1  rap guanine nucleotide exchange factor 6 isoform 4

    See identical proteins and their annotated locations for NP_001157860.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 4) is shorter than isoform 1.
    Source sequence(s)
    AF478567, AL832899, BC133703, DA817493
    Consensus CDS
    CCDS54899.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    Related
    ENSP00000487439.1, ENST00000627212.2
    Conserved Domains (6) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:8571081
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:749833
    UBQ; Ubiquitin-like proteins
  4. NM_001164389.2NP_001157861.1  rap guanine nucleotide exchange factor 6 isoform 5

    See identical proteins and their annotated locations for NP_001157861.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and 3' coding region, compared to variant 1. It encodes isoform 5 which has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC008497, AF478469, AF478567, AW204176, BX117281
    Consensus CDS
    CCDS54898.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    Related
    ENSP00000311419.6, ENST00000308008.10
    Conserved Domains (6) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:8571067
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:749833
    UBQ; Ubiquitin-like proteins
  5. NM_001164390.2NP_001157862.1  rap guanine nucleotide exchange factor 6 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 3' UTR and lacks a significant portion of the 3' coding region, compared to variant 1. This results in a protein (isoform 6) that maintains the reading frame but is shorter at the C-terminus, compared to isoform 1.
    Source sequence(s)
    AC004622, AF478567, BC142964
    Consensus CDS
    CCDS54897.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    Related
    ENSP00000425389.1, ENST00000510071.5
    Conserved Domains (6) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    COG0265
    Location:541609
    DegQ; Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:749827
    UBQ; Ubiquitin-like proteins
  6. NM_016340.6NP_057424.3  rap guanine nucleotide exchange factor 6 isoform 2

    See identical proteins and their annotated locations for NP_057424.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AF478567, AL832899, BC144627, DA817493
    Consensus CDS
    CCDS34225.1
    UniProtKB/Swiss-Prot
    Q8TEU7
    Related
    ENSP00000421684.1, ENST00000509018.5
    Conserved Domains (7) summary
    smart00229
    Location:412525
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    COG0664
    Location:274448
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:280380
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cd00155
    Location:8571067
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...
    cd00992
    Location:529609
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cl00047
    Location:3782
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl00155
    Location:749833
    UBQ; Ubiquitin-like proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    131423921..131635229 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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