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RGAG4 Gene

protein-coding   GIFtS: 40
GCID: GC0XM071263

Retrotransposon Gag Domain Containing 4

  Search for RGAG4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Retrotransposon Gag Domain Containing 41 2
6430402L03Rik2
MAR52
MART52
Retrotransposon Gag Domain-Containing Protein 42
KIAA20013

External Ids:    HGNC: 294301   Entrez Gene: 3405262   Ensembl: ENSG000002427327   UniProtKB: Q5HYW33   

Export aliases for RGAG4 gene to outside databases

Previous GC identifers: GC0XM071132 GC0XM065102


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RGAG4 Gene:
RGAG4 (retrotransposon gag domain containing 4) is a protein-coding gene. An important paralog of this gene is FAM127C.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the RGAG4 gene promoter:
         E2F-4   E2F-3a   E2F-5   E2F-2   Egr-4   MZF-1   E2F   E2F-1   COMP1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RGAG4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RGAG4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq13.1   Ensembl cytogenetic band:  Xq13.1   HGNC cytogenetic band: Xq13.1

RGAG4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RGAG4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM071263:  view genomic region     (about GC identifiers)

Start:
71,346,958 bp from pter      End:
71,351,758 bp from pter
Size:
4,801 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RGAG4_HUMAN, Q5HYW3 (See protein sequence)
Recommended Name: Retrotransposon gag domain-containing protein 4  
Size: 569 amino acids; 64711 Da
Sequence caution: Sequence=BAC02710.1; Type=Erroneous initiation;
Secondary accessions: A7E2W7 Q8NCM4 Q9NPX1

Explore the universe of human proteins at neXtProt for RGAG4: NX_Q5HYW3

Explore proteomics data for RGAG4 at MOPED


See RGAG4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001019626.1  
ENSEMBL proteins: 
 ENSP00000418667   ENSP00000476792   ENSP00000441366  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR005162 Retrotrans_gag_dom

Graphical View of Domain Structure for InterPro Entry Q5HYW3

ProtoNet protein and cluster: Q5HYW3


Find genes that share domains with RGAG4           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     2 GenomeRNAi human phenotypes for RGAG4:
 Increased G2M DNA content  S arrest 

Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidRGAG4 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
cytoskeleton1
extracellular1
mitochondrion1
peroxisome1
plasma membrane1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RGAG4
Interactions:

    Search GeneGlobe Interaction Network for RGAG4

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for RGAG4 (Q5HYW33 ENSP000004186674) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
DNM1LO004293, ENSP000002664814I2D: score=1 STRING: ENSP00000266481
MFN2O951403, ENSP000002353294I2D: score=1 STRING: ENSP00000235329
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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for RGAG4



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RGAG4 gene: 
NM_001024455.3  

Unigene Cluster for RGAG4:

Retrotransposon gag domain containing 4
Hs.512180  [show with all ESTs]
Unigene Representative Sequence: BC151224
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000479991(uc004eaj.2) ENST00000609883 ENST00000545866
miRNA
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SwitchGear 3'UTR luciferase reporter plasmidRGAG4 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AB082532.1 AL359579.2 BC151224.1 

3 DOTS entries:

DT.100742695  DT.455287  DT.97837243 

Selected AceView cDNA sequences (see all 59):

AL359579 AI887971 AA029003 AI204176 CK823539 BG820224 BM967353 BG820684 
BM720826 CA449911 AW206976 BM893994 AA927892 AA971871 BM673840 BM676932 
BF475306 CD513383 AI769062 BI195138 BE348492 AI351947 AW135185 BF526647 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RGAG4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGTTATTGTT
RGAG4 Expression
About this image


RGAG4 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Neural Tube (Nervous System)    fully expand to see all 2 entries
         Spinal Ventral Columns
RGAG4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RGAG4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.512180
    Custom PCR Arrays for RGAG4
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RGAG4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for RGAG4 gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rgag41 , 5 retrotransposon gag domain containing 41, 5 82.57(n)1
78.59(a)1
  X (45.06 cM)5
3314741  NM_001278534.11  NP_001265463.11 
 1020665445 


ENSEMBL Gene Tree for RGAG4 (if available)
TreeFam Gene Tree for RGAG4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RGAG4 gene
FAM127C2  LDOC1L2  LDOC12  FAM127B2  FAM127A2  
1 SIMAP similar gene for RGAG4 using alignment to 1 protein entry:     RGAG4_HUMAN:
LDOC1

Find genes that share paralogs with RGAG4           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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1 SNPs for RGAG4    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs66245951,2,4
----see VAR_0513192 mis40--------

HapMap Linkage Disequilibrium report for RGAG4 (71346958 - 71351758 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RGAG4: --
Locus Specific Mutation Databases (LSDB): RGAG4

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing RGAG4
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RGAG4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RGAG4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PubMed id 12056414)1, 2, 3 Ohara O.... Koseki H. (DNA Res. 2002)
  2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PubMed id 16093683)1, 3 Brandt J.... Volff J.-N. (Cytogenet. Genome Res. 2005)
  4. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. (PubMed id 15716091)1, 3 Brandt J.... Volff J.-N. (Gene 2005)
  5. Genome-scale RNAi screen for host factors required for HIV replication. (PubMed id 18976975)1 Zhou H....Espeseth A.S. (amp 2008)
  6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  7. MARCH-V is a novel mitofusin 2- and Drp1-binding protein able to change mitochondrial morphology. (PubMed id 16936636)1 Nakamura N.... Hirose S. (EMBO Rep. 2006)
  8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 340526 HGNC: 29430 AceView: RGAG4 Ensembl:ENSG00000242732 euGenes: HUgn340526
ECgene: RGAG4 H-InvDB: RGAG4

(According to HUGE)
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HUGE: KIAA2001

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RGAG4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RGAG4 gene:
Search GeneIP for patents involving RGAG4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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