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Aliases for RTL3 Gene

Aliases for RTL3 Gene

  • Retrotransposon Gag Like 3 2 3
  • Zinc Finger CCHC-Type Containing 5 2 3 5
  • ZCCHC5 3 4 5
  • Sushi-Ichi Retrotransposon Homolog 9 2 3
  • Mammalian Retrotransposon-Derived 3 2 3
  • Zinc Finger CCHC Domain-Containing Protein 5 3
  • Zinc Finger, CCHC Domain Containing 5 3
  • Mart3 3
  • SIRH9 3
  • Mar3 3
  • ZHC5 3

External Ids for RTL3 Gene

Previous HGNC Symbols for RTL3 Gene

  • ZCCHC5

Summaries for RTL3 Gene

Entrez Gene Summary for RTL3 Gene

  • This gene is a member of a family of gag-related retrotransposon genes. These genes appear to have lost the ability to retrotranspose; however, their open reading frames have remained intact, which may indicate that these genes have acquired new functions in the cell. [provided by RefSeq, Nov 2009]

GeneCards Summary for RTL3 Gene

RTL3 (Retrotransposon Gag Like 3) is a Protein Coding gene. An important paralog of this gene is RTL4.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTL3 Gene

Genomics for RTL3 Gene

Regulatory Elements for RTL3 Gene

Enhancers for RTL3 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
GH0XG079257 1.7 FANTOM5 Ensembl ENCODE dbSUPER 4.8 -599.9 -599882 4.7 PKNOX1 TBL1XR1 WRNIP1 BMI1 YBX1 RAD21 CBX5 ZNF207 RELB ETV6 GPR174 ITM2A RTL3 P2RY10 GC0XM079197 GC0XM079265
GH0XG079142 1.7 FANTOM5 Ensembl ENCODE dbSUPER 4.3 -491.2 -491215 15.5 TBP MXI1 TBL1XR1 MAX YBX1 ZBTB40 RELA ARID3A EGR1 POLR2A ITM2A P2RY10 GPR174 RTL3 LPAR4 GC0XM079072
GH0XG079159 1.2 Ensembl ENCODE dbSUPER 4.3 -504.8 -504751 9.0 PKNOX1 ZNF146 WRNIP1 ARID3A CBX5 IKZF2 CREM MTA2 CBFB BHLHE40 ITM2A RTL3 LPAR4 GPR174 GC0XM079072
GH0XG078657 0.6 Ensembl ENCODE 6.2 +0.3 261 2.7 MAFK RTL3 TAF9B UBE2V1P7
GH0XG079250 0.4 dbSUPER 4.9 -591.4 -591410 1.7 JUNB ETV6 GPR174 RTL3 GC0XM079197 GC0XM079265
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTL3 on UCSC Golden Path with GeneCards custom track

Genomic Location for RTL3 Gene

Chromosome:
X
Start:
78,656,069 bp from pter
End:
78,659,502 bp from pter
Size:
3,434 bases
Orientation:
Minus strand

Genomic View for RTL3 Gene

Genes around RTL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTL3 Gene

Proteins for RTL3 Gene

  • Protein details for RTL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N8U3-ZCHC5_HUMAN
    Recommended name:
    Zinc finger CCHC domain-containing protein 5
    Protein Accession:
    Q8N8U3
    Secondary Accessions:
    • B2RMZ0
    • Q5JQE9

    Protein attributes for RTL3 Gene

    Size:
    475 amino acids
    Molecular mass:
    52817 Da
    Quaternary structure:
    No Data Available

neXtProt entry for RTL3 Gene

Post-translational modifications for RTL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTL3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTL3 Gene

Domains & Families for RTL3 Gene

Protein Domains for RTL3 Gene

Suggested Antigen Peptide Sequences for RTL3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RTL3: view

No data available for UniProtKB/Swiss-Prot for RTL3 Gene

Function for RTL3 Gene

Gene Ontology (GO) - Molecular Function for RTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RTL3: view
genes like me logo Genes that share phenotypes with RTL3: view

Animal Model Products

miRNA for RTL3 Gene

miRTarBase miRNAs that target RTL3

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RTL3 Gene

Localization for RTL3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTL3 gene
Compartment Confidence
cytoskeleton 2
nucleus 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for RTL3 Gene

Pathways & Interactions for RTL3 Gene

No Data Available

Interacting Proteins for RTL3 Gene

Gene Ontology (GO) - Biological Process for RTL3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RTL3 Gene

Drugs & Compounds for RTL3 Gene

No Compound Related Data Available

Transcripts for RTL3 Gene

mRNA/cDNA for RTL3 Gene

(1) REFSEQ mRNAs :
(4) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTL3 Gene

No ASD Table

Relevant External Links for RTL3 Gene

GeneLoc Exon Structure for
RTL3
ECgene alternative splicing isoforms for
RTL3

Expression for RTL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RTL3 Gene:

RTL3
genes like me logo Genes that share expression patterns with RTL3: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTL3 Gene

Orthologs for RTL3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RTL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZCCHC5 34
  • 98.88 (n)
dog
(Canis familiaris)
Mammalia ZCCHC5 34
  • 75.58 (n)
cow
(Bos Taurus)
Mammalia ZCCHC5 34 35
  • 75.3 (n)
rat
(Rattus norvegicus)
Mammalia Zcchc5 34
  • 71.99 (n)
mouse
(Mus musculus)
Mammalia Zcchc5 34 16 35
  • 70.55 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 32 (a)
ManyToMany
-- 35
  • 31 (a)
ManyToMany
-- 35
  • 31 (a)
ManyToMany
-- 35
  • 31 (a)
ManyToMany
-- 35
  • 31 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 30 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 29 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 28 (a)
ManyToMany
-- 35
  • 27 (a)
ManyToMany
-- 35
  • 27 (a)
ManyToMany
-- 35
  • 27 (a)
ManyToMany
-- 35
  • 27 (a)
ManyToMany
-- 35
  • 26 (a)
ManyToMany
-- 35
  • 25 (a)
ManyToMany
-- 35
  • 22 (a)
ManyToMany
-- 35
  • 22 (a)
ManyToMany
-- 35
  • 22 (a)
ManyToMany
Species where no ortholog for RTL3 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)
  • 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 RTL3 Gene

ENSEMBL:
Gene Tree for RTL3 (if available)
TreeFam:
Gene Tree for RTL3 (if available)

Paralogs for RTL3 Gene

Paralogs for RTL3 Gene

genes like me logo Genes that share paralogs with RTL3: view

Variants for RTL3 Gene

Sequence variations from dbSNP and Humsavar for RTL3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1000025896 -- 78,656,274(+) AGTTC(C/T)GCAGG intron-variant, utr-variant-3-prime
rs1000373115 -- 78,660,189(+) TCAGT(A/T)CTGCA intron-variant, upstream-variant-2KB
rs1000407413 -- 78,659,779(+) TTCTT(G/T)GAAAA intron-variant, upstream-variant-2KB
rs1002048498 -- 78,658,393(+) AACAA(C/T)ATAGG intron-variant, reference, missense
rs1002696082 -- 78,659,472(+) CTGCA(A/T)GGAAA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RTL3 Gene

Variant ID Type Subtype PubMed ID
dgv517n21 CNV gain 19592680

Variation tolerance for RTL3 Gene

Residual Variation Intolerance Score: 84.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.28; 40.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTL3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTL3 Gene

Disorders for RTL3 Gene

Relevant External Links for RTL3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTL3

No disorders were found for RTL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTL3 Gene

Publications for RTL3 Gene

  1. 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
  2. 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
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 4 64

Products for RTL3 Gene

Sources for RTL3 Gene

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