Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CXCR7 (chemokine (C-X-C motif) receptor 7)

Identity

Other namesCMKOR1
RDC1
GPRN159
G protein-coupled receptor
chemokine orphan receptor 1
G protein-coupled receptor RDC1 homolog
HGNC (Hugo) CXCR7
LocusID (NCBI) 57007
Location 2q37.3
Location_base_pair Starts at 237478380 and ends at 237490994 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order Telomeric to IQCA
Centromeric to COPS8
Note RDC1 was originally thought to be the receptor for VIP.

DNA/RNA

Description The genomic size has been estimated to approximately 12.5-13.5 kb. RDC1 has previously been reported to contain only one exon of 1,09 kbp. However, the finding of a RDC1 transcript corresponding to four different regions with exon/intron boundaries in the BAC 514f21 suggests a more complex gene structure. The predicted amino acid sequence of exon 3 and 4 does not show any homology to the protein databases and, since they both contribute with stop codons, it could be questioned whether these sequences represent exons, or are part of an alternatively spliced 3' untranslated region of the gene.
Pseudogene None

Protein

Description 362 amino acids; 41522 Da
Expression RDC1 is expressed in embryological, juvenile as well as adult tissues. Expression has been reported in e.g. bladder, spleen, heart, skeletal muscle, peripheral nervous system and placenta.
Localisation Integral membrane protein
Function Orphan receptor, but its endogenous ligand has not yet been identified. The protein is also a coreceptor for human immunodeficiency viruses (HIV). RDC1 belongs to a family of G-protein coupled receptors, which includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide (G) binding proteins.
Homology RDC1 displays homology to other members of the large family of G-protein coupled receptors.

Mutations

Germinal Single nucleotide polymorphisms
Somatic Translocations involving RDC1 and HMGA2 has been reported in three lipomas (see below).

Implicated in

Entity Lipoma,
Disease Benign adipocyte tumor
Prognosis Good
Cytogenetics Translocations involving 2q35-37 and 12q13-15 have been reported in six lipomas
Hybrid/Mutated Gene Fusion between RDC1 and HMGA2 has been reported in three lipomas with rearrangement involving 2q35-37 and 12q13-15. The breakpoint occurred after the third exon of HMGA2, the most common breakpoint of this gene, and in a previously unknown 3' part of the RDC1 gene. The RDC1 part of the fusion was over 300 bp.
Abnormal Protein The functional impact of this fusion is most likely a truncation of HMGA2, since the RDC1 part contributes with a stop codon one amino acid downstream of the breakpoint.
Oncogenesis Not yet established
  
Entity Tenosynovial giant cell tumours
Disease Benign tumor of synovium and tendon sheath
Prognosis Good
Cytogenetics Translocations involving 1p11-13 and 2q35-37 have been reported in eight cases of tenosynovial giant cell tumours.
Hybrid/Mutated Gene Four out of seven cases of tenosynovial giant cell tumours with aberrations of 2q35-37 had breakpoints in a BAC probe 260J21 (BACPAC, Oakland), which contains the RDC1 gene.
  

External links

Nomenclature
HGNC (Hugo)CXCR7   23692
Entrez_Gene (NCBI)CXCR7  57007  chemokine (C-X-C motif) receptor 7
Cards
AtlasCMKOR1ID40108ch2q37
GeneCards (Weizmann)CXCR7
Ensembl (Hinxton)ENSG00000144476 [Gene_View]  chr2:237478380-237490994 [Contig_View]  CXCR7 [Vega]
AceView (NCBI)CXCR7
Genatlas (Paris)CXCR7
euGene (Indiana)57007
SOURCE (Stanford)NM_001047841 NM_020311
Genomic and cartography
GoldenPath (UCSC)CXCR7  -  2q37.3   chr2:237478380-237490994 +  2q37.3   [Description]    (hg19-Feb_2009)
EnsemblCXCR7 - 2q37.3 [CytoView]
Mapping of homologs : NCBICXCR7 [Mapview]
OMIM610376   
Gene and transcription
Genbank (Entrez)AF030297 AK291659 BC008459 BC036661 BM925428
RefSeq transcript (SRS)NM_001047841 NM_020311
RefSeq transcript (Entrez)NM_001047841 NM_020311
RefSeq genomic (SRS)AC_000134 NC_000002 NT_005120 NW_001838870
RefSeq genomic (Entrez)AC_000134 NC_000002 NT_005120 NW_001838870
Consensus coding sequences : CCDS (NCBI)CXCR7
Cluster EST : UnigeneHs.471751 [ SRS ] Hs.471751 [ NCBI ]
Alternative Splicing : Fast-db (Paris)16112
Alternative Splicing GalleryENSG00000144476
Gene ExpressionCXCR7 [ NCBI-GEO ]   CXCR7 [ EBI - ARRAY_EXPRESS ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP25106 (SRS) P25106 (Uniprot)
With graphics : InterProP25106
Splice isoforms : SwissVarP25106(Swissvar)
Domaine pattern : Prosite (SRS)G_PROTEIN_RECEP_F1_1 (PS00237)    G_PROTEIN_RECEP_F1_2 (PS50262)   
Domaine pattern : Prosite (Expaxy)G_PROTEIN_RECEP_F1_1 (PS00237)    G_PROTEIN_RECEP_F1_2 (PS50262)   
Domains : Interpro (SRS)7TM_GPCR_Rhodpsn    GPCR_Rhodpsn_supfam    RDC1_rcpt   
Domains : Interpro (EBI)7TM_GPCR_Rhodpsn    GPCR_Rhodpsn_supfam    RDC1_rcpt   
Related proteins : CluSTrP25106
Domain families : Pfam (SRS)7tm_1 (PF00001)   
Domain families : Pfam (Sanger)7tm_1 (PF00001)   
Domain families : Pfam (NCBI)pfam00001   
Blocks (Seattle)P25106
Human Protein AtlasENSG00000144476
HPRD09882
IPIIPI00012733   IPI00917980   
Protein Interaction databases
DIP (DOE-UCLA)P25106
IntAct (EBI)P25106
FunCoupENSG00000144476
REACTOMECXCR7
BioGRIDCXCR7
InParanoidP25106
Interologous Interaction database P25106
Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)CXCR7
SNP (GeneSNP Utah)CXCR7
SNP : HGBaseCXCR7
Genetic variants : HAPMAPCXCR7
Somatic Mutations in Cancer : COSMICCXCR7 
CONAN: Copy Number AnalysisCXCR7 
Mutations and Diseases : HGMDCXCR7
OMIM610376   
GENETests610376   
Disease Genetic AssociationCXCR7
Huge Navigator CXCR7 [HugePedia]  CXCR7 [HugeCancerGEM]
Genomic VariantsCXCR7
snp3D : Map Gene to Disease57007
General knowledge
Homologs : HomoloGeneCXCR7
Homology/Alignments : Family Browser (UCSC)CXCR7
Phylogenetic Trees/Animal Genes : TreeFamCXCR7
Chemical/Protein Interactions : CTD57007
Chemical/Pharm GKB GenePA162383053
Clinical trialCXCR7
Cancer Resource (Charite)ENSG00000144476
Ontology : AmiGOsignal transducer activity  receptor activity  G-protein coupled receptor activity  cytoplasm  early endosome  plasma membrane  cell adhesion  multicellular organismal development  integral to membrane  C-X-C chemokine receptor activity  negative regulation of apoptotic process  interspecies interaction between organisms  perinuclear region of cytoplasm  recycling endosome  chemokine-mediated signaling pathway  
Ontology : EGO-EBIsignal transducer activity  receptor activity  G-protein coupled receptor activity  cytoplasm  early endosome  plasma membrane  cell adhesion  multicellular organismal development  integral to membrane  C-X-C chemokine receptor activity  negative regulation of apoptotic process  interspecies interaction between organisms  perinuclear region of cytoplasm  recycling endosome  chemokine-mediated signaling pathway  
Other databases
Probes
Probes : ImagenesCXCR7 Related clones (RZPD - Berlin)
Litterature
PubMed54 Pubmed reference(s) in Entrez
PubGeneCXCR7
iHOPCXCR7

Bibliography

Cloning and expression of the human vasoactive intestinal peptide receptor.
Sreedharan SP, Robichon A, Peterson KE, Goetzl EJ
Proceedings of the National Academy of Sciences of the United States of America. 1991 ; 88 (11) : 4986-4990.
PMID 1675791
 
RDC1 may not be VIP receptor.
Nagata S, Ishihara T, Robberecht P, Libert F, Parmentier M, Christophe J, Vassart G
Trends in pharmacological sciences. 1992 ; 13 (3) : 102-103.
PMID 1315461
 
A putative G protein-coupled receptor, RDC1, is a novel coreceptor for human and simian immunodeficiency viruses.
Shimizu N, Soda Y, Kanbe K, Liu HY, Mukai R, Kitamura T, Hoshino H
Journal of virology. 2000 ; 74 (2) : 619-626.
PMID 10623723
 
Fusion of RDC1 with HMGA2 in lipomas as the result of chromosome aberrations involving 2q35-37 and 12q13-15.
Broberg K, Zhang M, Strˆmbeck B, Isaksson M, Nilsson M, Mertens F, Mandahl N, Panagopoulos I
International journal of oncology. 2002 ; 21 (2) : 321-326.
PMID 12118328
 
Molecular cytogenetic mapping of recurrent chromosomal breakpoints in tenosynovial giant cell tumors.
Nilsson M, Hˆglund M, Panagopoulos I, Sciot R, Dal Cin P, Debiec-Rychter M, Mertens F, Mandahl N
Virchows Archiv : an international journal of pathology. 2002 ; 441 (5) : 475-480.
PMID 12447678
 
Vascular gene expression in nonneoplastic and malignant brain.
Madden SL, Cook BP, Nacht M, Weber WD, Callahan MR, Jiang Y, Dufault MR, Zhang X, Zhang W, Walter-Yohrling J, Rouleau C, Akmaev VR, Wang CJ, Cao X, St Martin TB, Roberts BL, Teicher BA, Klinger KW, Stan RV, Lucey B, Carson-Walter EB, Laterra J, Walter KA
The American journal of pathology. 2004 ; 165 (2) : 601-608.
PMID 15277233
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written11-2004Karin Broberg

Citation

This paper should be referenced as such :
Broberg K . CXCR7 (chemokine (C-X-C motif) receptor 7). Atlas Genet Cytogenet Oncol Haematol. November 2004 .
URL : http://AtlasGeneticsOncology.org/Genes/CMKOR1ID40108ch2q37.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/38146/1/11-2004-CMKOR1ID40108ch2q37.pdf   [ Bibliographic record ]

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indexed on : Sat Apr 28 15:00:36 CEST 2012

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