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Aliases for RGAG4 Gene

Aliases for RGAG4 Gene

  • Retrotransposon Gag Domain Containing 4 2 3 5
  • Retrotransposon Gag Domain-Containing Protein 4 3
  • 6430402L03Rik 3
  • KIAA2001 4
  • MART5 3
  • MAR5 3

External Ids for RGAG4 Gene

Previous GeneCards Identifiers for RGAG4 Gene

  • GC0XM071132
  • GC0XM071263
  • GC0XM065102

Summaries for RGAG4 Gene

GeneCards Summary for RGAG4 Gene

RGAG4 (Retrotransposon Gag Domain Containing 4) is a Protein Coding gene. An important paralog of this gene is LDOC1L.

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RGAG4 Gene

Genomics for RGAG4 Gene

Regulatory Elements for RGAG4 Gene

Enhancers for RGAG4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF072107 1.1 FANTOM5 Ensembl ENCODE 41.4 +23.9 23907 1.2 CTCF KLF17 ZIC2 RAD21 ZNF324 ZFHX2 GLIS2 ZBTB48 PATZ1 PRDM10 RGAG4 FLJ44635 ERCC6L LOC100420758 ENSG00000229601 OGT LOC392489 NHSL2 PIR32507 PIR46676
GH0XF072001 0.6 ENCODE 32.4 +130.3 130276 0.2 ZNF202 ZNF680 ZFP64 ZBTB11 ZNF140 ZBTB8A REST ZNF623 ZNF518A ZNF781 RGAG4 NHSL2 ERCC6L OGT LOC100420758 ENSG00000229601 RNU6-1078P GC0XM071966 RPS26P11
GH0XF071180 1.4 FANTOM5 Ensembl ENCODE 19.4 +949.3 949261 3.9 PKNOX1 ZFP64 SIN3A ARID4B FEZF1 DMAP1 YY1 FOS SP3 NFYC LOC100420758 OGT P2RY4 ENSG00000229601 RGAG4 RPS23P8 LOC392489 SNX12 IL2RG GJB1
GH0XF072168 1.3 Ensembl ENCODE 16.6 -37.3 -37261 1.2 TFDP1 L3MBTL2 MGA RGAG4 NHSL2 ERCC6L ENSG00000225471 PIN4
GH0XF072018 1.2 Ensembl ENCODE 13.4 +112.4 112370 3.1 ELF3 CBX3 CREB3L1 ZNF48 RAD21 RARA GLIS2 EGR1 ZNF143 RCOR1 NHSL2 RGAG4 RPS26P11 RNU6-1078P GC0XM071966
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RGAG4 on UCSC Golden Path with GeneCards custom track

Promoters for RGAG4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001917667 201 1800 CTCF RAD21 E2F1 ZFHX2 GLIS2 POLR2A ZNF366 PATZ1 SCRT2 PRDM10

Genomic Location for RGAG4 Gene

Chromosome:
X
Start:
72,127,110 bp from pter
End:
72,131,901 bp from pter
Size:
4,792 bases
Orientation:
Minus strand

Genomic View for RGAG4 Gene

Genes around RGAG4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGAG4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGAG4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGAG4 Gene

Proteins for RGAG4 Gene

  • Protein details for RGAG4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5HYW3-RGAG4_HUMAN
    Recommended name:
    Retrotransposon gag domain-containing protein 4
    Protein Accession:
    Q5HYW3
    Secondary Accessions:
    • A7E2W7
    • Q8NCM4
    • Q9NPX1

    Protein attributes for RGAG4 Gene

    Size:
    569 amino acids
    Molecular mass:
    64711 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC02710.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for RGAG4 Gene

Post-translational modifications for RGAG4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RGAG4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RGAG4 Gene

Domains & Families for RGAG4 Gene

Protein Domains for RGAG4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RGAG4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RGAG4: view

No data available for Gene Families and UniProtKB/Swiss-Prot for RGAG4 Gene

Function for RGAG4 Gene

Phenotypes for RGAG4 Gene

genes like me logo Genes that share phenotypes with RGAG4: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RGAG4 Gene

Localization for RGAG4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RGAG4 Gene COMPARTMENTS Subcellular localization image for RGAG4 gene
Compartment Confidence
cytosol 3
nucleus 3
cytoskeleton 1
extracellular 1
golgi apparatus 1
mitochondrion 1
peroxisome 1
plasma membrane 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for RGAG4 Gene

Pathways & Interactions for RGAG4 Gene

SuperPathways for RGAG4 Gene

No Data Available

Interacting Proteins for RGAG4 Gene

Gene Ontology (GO) - Biological Process for RGAG4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RGAG4 Gene

Transcripts for RGAG4 Gene

mRNA/cDNA for RGAG4 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(59) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RGAG4 Gene

Retrotransposon gag domain containing 4:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RGAG4 Gene

No ASD Table

Relevant External Links for RGAG4 Gene

GeneLoc Exon Structure for
RGAG4
ECgene alternative splicing isoforms for
RGAG4

Expression for RGAG4 Gene

mRNA expression in normal human tissues for RGAG4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RGAG4 Gene

This gene is overexpressed in Bone (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RGAG4 Gene



Protein tissue co-expression partners for RGAG4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RGAG4 Gene:

RGAG4

SOURCE GeneReport for Unigene cluster for RGAG4 Gene:

Hs.512180
genes like me logo Genes that share expression patterns with RGAG4: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RGAG4 Gene

Orthologs for RGAG4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for RGAG4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RGAG4 34 35
  • 97.93 (n)
mouse
(Mus musculus)
Mammalia Rgag4 34 16 35
  • 82.57 (n)
cow
(Bos Taurus)
Mammalia RGAG4 34 35
  • 82.23 (n)
dog
(Canis familiaris)
Mammalia RGAG4 34 35
  • 82.21 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911832 34
  • 81.3 (n)
Species where no ortholog for RGAG4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for RGAG4 Gene

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

Paralogs for RGAG4 Gene

Paralogs for RGAG4 Gene

(1) SIMAP similar genes for RGAG4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with RGAG4: view

Variants for RGAG4 Gene

Sequence variations from dbSNP and Humsavar for RGAG4 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs10126749 -- 72,129,512(+) AGGGG(A/G)AATAC intron-variant, utr-variant-3-prime
rs111314598 -- 72,131,763(+) TCGCC(C/G)GGGCC intron-variant, utr-variant-5-prime
rs111377644 -- 72,131,796(+) GGGCC(C/T)GGAGG intron-variant, utr-variant-5-prime
rs1127428 -- 72,127,290(-) TGAAA(A/G)AGGGG intron-variant, utr-variant-3-prime
rs11345558 -- 72,133,554(+) CTTCA(-/C)CTTAG intron-variant, upstream-variant-2KB

Variation tolerance for RGAG4 Gene

Residual Variation Intolerance Score: 90.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.64; 65.63% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RGAG4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGAG4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RGAG4 Gene

Disorders for RGAG4 Gene

Relevant External Links for RGAG4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RGAG4

No disorders were found for RGAG4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RGAG4 Gene

Publications for RGAG4 Gene

  1. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PMID: 12056414) Ohara O. … Koseki H. (DNA Res. 2002) 2 3 4 64
  2. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. (PMID: 15716091) Brandt J. … Volff J.-N. (Gene 2005) 2 3 64
  3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PMID: 16093683) Brandt J. … Volff J.-N. (Cytogenet. Genome Res. 2005) 2 3 64
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 3 4 64
  5. Genome-scale RNAi screen for host factors required for HIV replication. (PMID: 18976975) Zhou H. … Espeseth A.S. (Cell Host Microbe 2008) 3 64

Products for RGAG4 Gene

Sources for RGAG4 Gene

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