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

Gene ID: 2889, updated on 5-Mar-2024

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; AllianceGenome:HGNC:4568
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
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Genomic context

See RAPGEF1 in Genome Data Viewer
Location:
9q34.13
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (131576775..131740076, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (143789743..143952984, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (134452162..134615463, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:134403902-134405101 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134405807-134406720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20421 Neighboring gene NANOG hESC enhancer GRCh37_chr9:134426802-134427303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134443475-134443974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29193 Neighboring gene uridine-cytidine kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134464737-134465236 Neighboring gene proline rich transmembrane protein 1B Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134481176-134481676 Neighboring gene Sharpr-MPRA regulatory region 10461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134493979-134494945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134499860-134500360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134504170-134504919 Neighboring gene Sharpr-MPRA regulatory region 12258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134530670-134531170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134534752-134535285 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134535286-134535818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29207 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:134558729-134559329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134584807-134585588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587455-134587956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587957-134588456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134598083-134598582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20422 Neighboring gene Sharpr-MPRA regulatory region 1247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29213 Neighboring gene Sharpr-MPRA regulatory region 10210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29214 Neighboring gene RNA, 7SL, cytoplasmic 328, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134630482-134631089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134669412-134669916 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:134674709-134674899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134680399-134680898 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134682767-134683702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134689077-134689577 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134692257-134692758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134703449-134703948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134713047-134713585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134730057-134731006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134731007-134731954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134752115-134752615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134764767-134765298 Neighboring gene Sharpr-MPRA regulatory region 801 Neighboring gene mediator complex subunit 27 Neighboring gene NANOG hESC enhancer GRCh37_chr9:134840462-134840963 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:134843516-134843723 Neighboring gene MPRA-validated peak7336 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:134882251-134882943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134915689-134916190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134916191-134916690 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:134917173-134918372 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:134951028-134952227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29216

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

Clone Names

  • DKFZp781P1719

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
 
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
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)

NEW Try the new Transcript table

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_050622.2 RefSeqGene

    Range
    5000..168301
    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
    Consensus CDS
    CCDS94521.1
    UniProtKB/TrEMBL
    A0A804HL87
    Related
    ENSP00000508246.1, ENST00000683357.1
    Conserved Domains (3) summary
    smart00147
    Location:10221251
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:8741015
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    PHA03247
    Location:227824
    PHA03247; large tegument protein UL36; Provisional
  3. NM_001377936.1NP_001364865.1  rap guanine nucleotide exchange factor 1 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL160276
    UniProtKB/TrEMBL
    A0A1S5UYZ7
    Conserved Domains (3) summary
    smart00147
    Location:8351064
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:687828
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    PHA03247
    Location:179437
    PHA03247; large tegument protein UL36; Provisional
  4. NM_001377937.1NP_001364866.1  rap guanine nucleotide exchange factor 1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
    Conserved Domains (3) summary
    smart00147
    Location:8151044
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:667808
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    PHA03247
    Location:190448
    PHA03247; large tegument protein UL36; Provisional
  5. NM_001377938.1NP_001364867.1  rap guanine nucleotide exchange factor 1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL160271, AL160276
    Conserved Domains (4) summary
    smart00147
    Location:9851214
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases
    smart00229
    Location:837978
    RasGEFN; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif
    PHA03247
    Location:190448
    PHA03247; large tegument protein UL36; Provisional
    PHA03307
    Location:675846
    PHA03307; transcriptional regulator ICP4; Provisional
  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, Q5JUE4, Q68DL3, Q8IV73
    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, ENST00000372190.8
    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: 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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    131576775..131740076 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005272186.5XP_005272243.1  rap guanine nucleotide exchange factor 1 isoform X4

    See identical proteins and their annotated locations for XP_005272243.1

    Conserved Domains (4) 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
    PHA03247
    Location:228486
    PHA03247; large tegument protein UL36; Provisional
    PHA03307
    Location:713884
    PHA03307; transcriptional regulator ICP4; Provisional
  2. XM_011518572.3XP_011516874.1  rap guanine nucleotide exchange factor 1 isoform X2

    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_047423252.1XP_047279208.1  rap guanine nucleotide exchange factor 1 isoform X10

    Related
    ENST00000419442.2
  4. XM_017014633.2XP_016870122.1  rap guanine nucleotide exchange factor 1 isoform X5

  5. XM_047423251.1XP_047279207.1  rap guanine nucleotide exchange factor 1 isoform X9

  6. XM_011518571.3XP_011516873.1  rap guanine nucleotide exchange factor 1 isoform X1

    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
  7. XM_047423254.1XP_047279210.1  rap guanine nucleotide exchange factor 1 isoform X18

  8. XM_024447521.2XP_024303289.1  rap guanine nucleotide exchange factor 1 isoform X17

    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
  9. XM_006717072.4XP_006717135.1  rap guanine nucleotide exchange factor 1 isoform X8

    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
  10. XM_006717074.4XP_006717137.1  rap guanine nucleotide exchange factor 1 isoform X16

    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
  11. XM_047423253.1XP_047279209.1  rap guanine nucleotide exchange factor 1 isoform X14

  12. XM_006717067.4XP_006717130.1  rap guanine nucleotide exchange factor 1 isoform X3

    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
  13. XM_011518579.4XP_011516881.1  rap guanine nucleotide exchange factor 1 isoform X15

    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
  14. XM_011518578.4XP_011516880.1  rap guanine nucleotide exchange factor 1 isoform X13

    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
  15. XM_011518577.4XP_011516879.1  rap guanine nucleotide exchange factor 1 isoform X12

    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_011518576.4XP_011516878.1  rap guanine nucleotide exchange factor 1 isoform X11

    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
  17. XM_017014636.3XP_016870125.1  rap guanine nucleotide exchange factor 1 isoform X7

  18. XM_017014635.3XP_016870124.1  rap guanine nucleotide exchange factor 1 isoform X6

  19. XM_011518581.4XP_011516883.1  rap guanine nucleotide exchange factor 1 isoform X19

    Conserved Domains (1) summary
    PHA03247
    Location:242500
    PHA03247; large tegument protein UL36; Provisional
  20. XM_047423255.1XP_047279211.1  rap guanine nucleotide exchange factor 1 isoform X21

  21. XM_011518582.4XP_011516884.1  rap guanine nucleotide exchange factor 1 isoform X20

    Conserved Domains (1) summary
    PHA03247
    Location:242500
    PHA03247; large tegument protein UL36; Provisional
  22. XM_047423256.1XP_047279212.1  rap guanine nucleotide exchange factor 1 isoform X22

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    143789743..143952984 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362783.1XP_054218758.1  rap guanine nucleotide exchange factor 1 isoform X4

  2. XM_054362781.1XP_054218756.1  rap guanine nucleotide exchange factor 1 isoform X2

  3. XM_054362788.1XP_054218763.1  rap guanine nucleotide exchange factor 1 isoform X10

  4. XM_054362784.1XP_054218759.1  rap guanine nucleotide exchange factor 1 isoform X5

  5. XM_054362787.1XP_054218762.1  rap guanine nucleotide exchange factor 1 isoform X9

  6. XM_054362780.1XP_054218755.1  rap guanine nucleotide exchange factor 1 isoform X1

  7. XM_054362786.1XP_054218761.1  rap guanine nucleotide exchange factor 1 isoform X8

  8. XM_054362782.1XP_054218757.1  rap guanine nucleotide exchange factor 1 isoform X3

  9. XM_054362790.1XP_054218765.1  rap guanine nucleotide exchange factor 1 isoform X12

  10. XM_054362789.1XP_054218764.1  rap guanine nucleotide exchange factor 1 isoform X11

  11. XM_054362791.1XP_054218766.1  rap guanine nucleotide exchange factor 1 isoform X13

  12. XM_054362795.1XP_054218770.1  rap guanine nucleotide exchange factor 1 isoform X17

  13. XM_054362792.1XP_054218767.1  rap guanine nucleotide exchange factor 1 isoform X14

  14. XM_054362793.1XP_054218768.1  rap guanine nucleotide exchange factor 1 isoform X15

  15. XM_054362796.1XP_054218771.1  rap guanine nucleotide exchange factor 1 isoform X18

  16. XM_054362794.1XP_054218769.1  rap guanine nucleotide exchange factor 1 isoform X16

  17. XM_054362785.1XP_054218760.1  rap guanine nucleotide exchange factor 1 isoform X7

  18. XM_054362797.1XP_054218772.1  rap guanine nucleotide exchange factor 1 isoform X19

  19. XM_054362798.1XP_054218773.1  rap guanine nucleotide exchange factor 1 isoform X20

  20. XM_054362799.1XP_054218774.1  rap guanine nucleotide exchange factor 1 isoform X21

  21. XM_054362800.1XP_054218775.1  rap guanine nucleotide exchange factor 1 isoform X22