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RAPGEF1 Rap guanine nucleotide exchange factor 1 [ Homo sapiens (human) ]

Gene ID: 2889, updated on 24-Nov-2020

Summary

Official Symbol
RAPGEF1provided by HGNC
Official Full Name
Rap guanine nucleotide exchange factor 1provided by HGNC
Primary source
HGNC:HGNC:4568
See related
Ensembl:ENSG00000107263 MIM:600303
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
C3G; GRF2
Summary
This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 13.7), lymph node (RPKM 12.3) and 25 other tissues See more
Orthologs

Genomic context

See RAPGEF1 in Genome Data Viewer
Location:
9q34.13
Exon count:
37
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (131576770..131740076, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (134452157..134615364, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene protein O-mannosyltransferase 1 Neighboring gene uridine-cytidine kinase 1 Neighboring gene proline rich transmembrane protein 1B Neighboring gene Sharpr-MPRA regulatory region 10461 Neighboring gene Sharpr-MPRA regulatory region 12258 Neighboring gene Sharpr-MPRA regulatory region 10210 Neighboring gene RNA, 7SL, cytoplasmic 328, pseudogene Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 3 Neighboring gene mediator complex subunit 27

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 1 (RAPGEF1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp781P1719

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SH3 domain binding IEA
Inferred from Electronic Annotation
more info
 
guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Rap protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
activation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
activation of MAPKK activity TAS
Traceable Author Statement
more info
 
blood vessel development IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cellular response to cAMP IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to nerve growth factor stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
establishment of endothelial barrier IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
 
negative regulation of Ras protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
negative regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein kinase B signaling IEA
Inferred from Electronic Annotation
more info
 
nerve growth factor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
platelet-derived growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
 
positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of Ras protein signal transduction TAS
Traceable Author Statement
more info
 
positive regulation of neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of JNK cascade IEA
Inferred from Electronic Annotation
more info
 
regulation of cell junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
transmembrane receptor protein tyrosine kinase signaling pathway TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
phagocytic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
rap guanine nucleotide exchange factor 1
Names
CRK SH3-binding GNRP
Rap guanine nucleotide exchange factor (GEF) 1
guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)

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.

Genomic

  1. NG_050622.1 RefSeqGene

    Range
    5001..168175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304275.2NP_001291204.1  rap guanine nucleotide exchange factor 1 isoform c

    See identical proteins and their annotated locations for NP_001291204.1

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
    Consensus CDS
    CCDS78450.1
    UniProtKB/Swiss-Prot
    Q13905
    Related
    ENSP00000361269.1, ENST00000372195.5
    Conserved Domains (2) summary
    smart00147
    Location:8531082
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:705846
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  2. NM_001377935.1NP_001364864.1  rap guanine nucleotide exchange factor 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
  3. NM_001377936.1NP_001364865.1  rap guanine nucleotide exchange factor 1 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL160276
  4. NM_001377937.1NP_001364866.1  rap guanine nucleotide exchange factor 1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
  5. NM_001377938.1NP_001364867.1  rap guanine nucleotide exchange factor 1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
  6. NM_005312.4NP_005303.2  rap guanine nucleotide exchange factor 1 isoform a

    See identical proteins and their annotated locations for NP_005303.2

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
    Consensus CDS
    CCDS48047.1
    UniProtKB/Swiss-Prot
    Q13905
    Related
    ENSP00000361263.2, ENST00000372189.7
    Conserved Domains (2) summary
    smart00147
    Location:8361065
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:688829
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  7. NM_198679.2NP_941372.1  rap guanine nucleotide exchange factor 1 isoform b

    See identical proteins and their annotated locations for NP_941372.1

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
    Consensus CDS
    CCDS48048.1
    UniProtKB/Swiss-Prot
    Q13905
    Related
    ENSP00000361264.3, ENST00000372190.7
    Conserved Domains (2) summary
    smart00147
    Location:8541083
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:706847
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif

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_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    131576770..131740076 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005272186.4XP_005272243.1  rap guanine nucleotide exchange factor 1 isoform X6

    See identical proteins and their annotated locations for XP_005272243.1

    Conserved Domains (2) summary
    smart00147
    Location:10231252
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8751016
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  2. XM_011518572.2XP_011516874.1  rap guanine nucleotide exchange factor 1 isoform X4

    Conserved Domains (2) summary
    smart00147
    Location:10311260
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8831024
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  3. XM_017014633.1XP_016870122.1  rap guanine nucleotide exchange factor 1 isoform X8

  4. XM_011518573.3XP_011516875.1  rap guanine nucleotide exchange factor 1 isoform X7

    Conserved Domains (2) summary
    smart00147
    Location:10141243
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8661007
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  5. XM_011518571.2XP_011516873.1  rap guanine nucleotide exchange factor 1 isoform X3

    Conserved Domains (2) summary
    smart00147
    Location:10321261
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8841025
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  6. XM_011518569.3XP_011516871.1  rap guanine nucleotide exchange factor 1 isoform X1

    Conserved Domains (2) summary
    smart00147
    Location:10371266
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8891030
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  7. XM_024447521.1XP_024303289.1  rap guanine nucleotide exchange factor 1 isoform X23

    Conserved Domains (3) summary
    smart00147
    Location:8521081
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:704845
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    cl26464
    Location:196454
    Atrophin-1; Atrophin-1 family
  8. XM_006717072.3XP_006717135.1  rap guanine nucleotide exchange factor 1 isoform X13

    Conserved Domains (2) summary
    smart00147
    Location:9911220
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:843984
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  9. XM_006717074.3XP_006717137.1  rap guanine nucleotide exchange factor 1 isoform X22

    Conserved Domains (2) summary
    smart00147
    Location:8591088
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:711852
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  10. XM_006717067.3XP_006717130.1  rap guanine nucleotide exchange factor 1 isoform X5

    Conserved Domains (2) summary
    smart00147
    Location:10291258
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8811022
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  11. XM_011518579.3XP_011516881.1  rap guanine nucleotide exchange factor 1 isoform X21

    Conserved Domains (2) summary
    smart00147
    Location:8671096
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:719860
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  12. XM_011518578.3XP_011516880.1  rap guanine nucleotide exchange factor 1 isoform X20

    Conserved Domains (2) summary
    smart00147
    Location:8981127
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:750891
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  13. XM_017014638.2XP_016870127.1  rap guanine nucleotide exchange factor 1 isoform X16

  14. XM_017014637.2XP_016870126.1  rap guanine nucleotide exchange factor 1 isoform X15

  15. XM_011518577.3XP_011516879.1  rap guanine nucleotide exchange factor 1 isoform X19

    Conserved Domains (2) summary
    smart00147
    Location:9191148
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:771912
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  16. XM_011518575.3XP_011516877.1  rap guanine nucleotide exchange factor 1 isoform X10

    Conserved Domains (2) summary
    smart00147
    Location:10051234
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:857998
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  17. XM_011518570.3XP_011516872.1  rap guanine nucleotide exchange factor 1 isoform X2

    Conserved Domains (2) summary
    smart00147
    Location:10361265
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8881029
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  18. XM_011518576.3XP_011516878.1  rap guanine nucleotide exchange factor 1 isoform X18

    Conserved Domains (2) summary
    smart00147
    Location:9201149
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:772913
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  19. XM_017014639.2XP_016870128.1  rap guanine nucleotide exchange factor 1 isoform X17

  20. XM_011518574.3XP_011516876.1  rap guanine nucleotide exchange factor 1 isoform X9

    Conserved Domains (2) summary
    smart00147
    Location:10061235
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:858999
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
  21. XM_017014635.2XP_016870124.1  rap guanine nucleotide exchange factor 1 isoform X11

  22. XM_017014636.2XP_016870125.1  rap guanine nucleotide exchange factor 1 isoform X12

  23. XM_017014634.1XP_016870123.1  rap guanine nucleotide exchange factor 1 isoform X11

  24. XM_017014640.2XP_016870129.1  rap guanine nucleotide exchange factor 1 isoform X24

  25. XM_017014641.2XP_016870130.1  rap guanine nucleotide exchange factor 1 isoform X25

  26. XM_011518580.3XP_011516882.1  rap guanine nucleotide exchange factor 1 isoform X26

    Conserved Domains (1) summary
    PHA03247
    Location:242500
    PHA03247; large tegument protein UL36; Provisional
  27. XM_011518581.3XP_011516883.1  rap guanine nucleotide exchange factor 1 isoform X27

    Conserved Domains (1) summary
    PHA03247
    Location:242500
    PHA03247; large tegument protein UL36; Provisional
  28. XM_011518582.3XP_011516884.1  rap guanine nucleotide exchange factor 1 isoform X28

    Conserved Domains (1) summary
    PHA03247
    Location:242500
    PHA03247; large tegument protein UL36; Provisional

RNA

  1. XR_001746282.2 RNA Sequence

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