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Aliases for ELL3 Gene

Aliases for ELL3 Gene

  • Elongation Factor For RNA Polymerase II 3 2 3 5
  • Elongation Factor RNA Polymerase II-Like 3 2 3
  • RNA Polymerase II Elongation Factor ELL3 3

External Ids for ELL3 Gene

Previous GeneCards Identifiers for ELL3 Gene

  • GC15M041643
  • GC15M041780
  • GC15M041852
  • GC15M044064
  • GC15M020888

Summaries for ELL3 Gene

GeneCards Summary for ELL3 Gene

ELL3 (Elongation Factor For RNA Polymerase II 3) is a Protein Coding gene. Among its related pathways are Formation of HIV-1 elongation complex containing HIV-1 Tat and Gene Expression. Gene Ontology (GO) annotations related to this gene include enhancer binding. An important paralog of this gene is ELL2.

UniProtKB/Swiss-Prot for ELL3 Gene

  • Enhancer-binding elongation factor that specifically binds enhancers in embryonic stem cells (ES cells), marks them, and is required for their future activation during stem cell specification. Does not only bind to enhancer regions of active genes, but also marks the enhancers that are in a poised or inactive state in ES cells and is required for establishing proper RNA polymerase II occupancy at developmentally regulated genes in a cohesin-dependent manner. Probably required for priming developmentally regulated genes for later recruitment of the super elongation complex (SEC), for transcriptional activation during differentiation. Required for recruitment of P-TEFb within SEC during differentiation. Probably preloaded on germ cell chromatin, suggesting that it may prime gene activation by marking enhancers as early as in the germ cells. Promoting epithelial-mesenchymal transition (EMT) (By similarity). Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968).

Additional gene information for ELL3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ELL3 Gene

Genomics for ELL3 Gene

GeneHancer (GH) Regulatory Elements for ELL3 Gene

Promoters and enhancers for ELL3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J043791 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 650.4 -19.0 -18972 10.6 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 SP3 NFYC MEF2D SERINC4 GC15P043795 HYPK PIR54305 GC15M043788 ELL3 SERF2 SPG11 CTDSPL2 ENSG00000259563
GH15J043774 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +1.1 1069 3.6 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 ZNF207 ELL3 SERF2 WDR76 ADAL SPG11 STRC ENSG00000259563 CTDSPL2 MFAP1 ENSG00000262560
GH15J043823 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 24.4 -48.5 -48485 5.7 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 GLIS1 NBN WDR76 MFAP1 CTDSPL2 SPG11 ZSCAN29 ENSG00000259563 LCMT2 ENSG00000249839 ELL3 ADAL
GH15J044286 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 14.3 -511.3 -511250 3.7 HDGF PKNOX1 SMAD1 NEUROD1 SIN3A FEZF1 DMAP1 IRF4 YY1 ZNF207 CASC4 GC15M044288 CTDSPL2 LCMT2 ENSG00000259563 ZSCAN29 WDR76 SPG11 TUBGCP4 ENSG00000249839
GH15J043745 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.9 +30.6 30642 2.6 HDGF ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF143 SP3 SP5 NFYC PDIA3 CATSPER2P1 STRCP1 CTDSPL2 WDR76 MFAP1 SPG11 LCMT2 ELL3 ZSCAN29
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ELL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ELL3 gene promoter:
  • AREB6
  • Pax-4a
  • Spz1
  • GATA-1
  • AML1a
  • GR
  • GR-alpha
  • GR-beta
  • RREB-1

Genomic Locations for ELL3 Gene

Genomic Locations for ELL3 Gene
chr15:43,772,600-43,777,543
(GRCh38/hg38)
Size:
4,944 bases
Orientation:
Minus strand
chr15:44,064,798-44,069,741
(GRCh37/hg19)
Size:
4,944 bases
Orientation:
Minus strand

Genomic View for ELL3 Gene

Genes around ELL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ELL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ELL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ELL3 Gene

Proteins for ELL3 Gene

  • Protein details for ELL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HB65-ELL3_HUMAN
    Recommended name:
    RNA polymerase II elongation factor ELL3
    Protein Accession:
    Q9HB65
    Secondary Accessions:
    • B3KQ66
    • B3KX08
    • Q6I9Z7
    • Q9H634

    Protein attributes for ELL3 Gene

    Size:
    397 amino acids
    Molecular mass:
    45361 Da
    Quaternary structure:
    • Interacts with AFF4 (By similarity). Component of the super elongation complex (SEC), at least composed of EAF1, EAF2, CDK9, MLLT3/AF9, AFF (AFF1 or AFF4), the P-TEFb complex and ELL (ELL, ELL2 or ELL3). Component of the little elongation complex (LEC), at least composed of ELL (ELL, ELL2 or ELL3), ZC3H8, ICE1 and ICE2.

    Alternative splice isoforms for ELL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ELL3 Gene

Post-translational modifications for ELL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ELL3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ELL3 Gene

Domains & Families for ELL3 Gene

Gene Families for ELL3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ELL3 Gene

Suggested Antigen Peptide Sequences for ELL3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HB65

UniProtKB/Swiss-Prot:

ELL3_HUMAN :
  • Belongs to the ELL/occludin family.
Family:
  • Belongs to the ELL/occludin family.
genes like me logo Genes that share domains with ELL3: view

Function for ELL3 Gene

Molecular function for ELL3 Gene

UniProtKB/Swiss-Prot Function:
Enhancer-binding elongation factor that specifically binds enhancers in embryonic stem cells (ES cells), marks them, and is required for their future activation during stem cell specification. Does not only bind to enhancer regions of active genes, but also marks the enhancers that are in a poised or inactive state in ES cells and is required for establishing proper RNA polymerase II occupancy at developmentally regulated genes in a cohesin-dependent manner. Probably required for priming developmentally regulated genes for later recruitment of the super elongation complex (SEC), for transcriptional activation during differentiation. Required for recruitment of P-TEFb within SEC during differentiation. Probably preloaded on germ cell chromatin, suggesting that it may prime gene activation by marking enhancers as early as in the germ cells. Promoting epithelial-mesenchymal transition (EMT) (By similarity). Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968).

Gene Ontology (GO) - Molecular Function for ELL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21729782
GO:0035326 enhancer binding ISS,IEA --
genes like me logo Genes that share ontologies with ELL3: view
genes like me logo Genes that share phenotypes with ELL3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ELL3 Gene

Localization for ELL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ELL3 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 ELL3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ELL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 10882741
GO:0005654 nucleoplasm TAS,IDA --
GO:0005730 nucleolus IDA --
GO:0008023 transcription elongation factor complex IEA,NAS 10882741
genes like me logo Genes that share ontologies with ELL3: view

Pathways & Interactions for ELL3 Gene

genes like me logo Genes that share pathways with ELL3: view

Pathways by source for ELL3 Gene

Gene Ontology (GO) - Biological Process for ELL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006354 DNA-templated transcription, elongation IDA 10882741
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II ISS,IEA --
GO:0006368 transcription elongation from RNA polymerase II promoter IEA,IDA 10882741
genes like me logo Genes that share ontologies with ELL3: view

No data available for SIGNOR curated interactions for ELL3 Gene

Drugs & Compounds for ELL3 Gene

No Compound Related Data Available

Transcripts for ELL3 Gene

mRNA/cDNA for ELL3 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(1824) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ELL3 Gene

Elongation factor RNA polymerase II-like 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ELL3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c
SP1: - - -
SP2: -
SP3: -
SP4:
SP5: - -
SP6: - -
SP7: - - - -

Relevant External Links for ELL3 Gene

GeneLoc Exon Structure for
ELL3
ECgene alternative splicing isoforms for
ELL3

Expression for ELL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ELL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ELL3 Gene

This gene is overexpressed in CD4 Tcells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ELL3 Gene



Protein tissue co-expression partners for ELL3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ELL3 Gene:

ELL3

SOURCE GeneReport for Unigene cluster for ELL3 Gene:

Hs.706346

mRNA Expression by UniProt/SwissProt for ELL3 Gene:

Q9HB65-ELL3_HUMAN
Tissue specificity: Testis specific.

Evidence on tissue expression from TISSUES for ELL3 Gene

  • Nervous system(3.5)
  • Lung(3.2)
genes like me logo Genes that share expression patterns with ELL3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ELL3 Gene

Orthologs for ELL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ELL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ELL3 34 33
  • 99.5 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ELL3 34 33
  • 87.85 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ELL3 34 33
  • 86.99 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ell3 33
  • 83.12 (n)
mouse
(Mus musculus)
Mammalia Ell3 16 34 33
  • 82.99 (n)
oppossum
(Monodelphis domestica)
Mammalia ELL3 34
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ELL3 34
  • 35 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii ELL3 34
  • 21 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Su(Tpl) 34
  • 8 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1855 34
  • 19 (a)
OneToMany
Species where no ortholog for ELL3 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)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for ELL3 Gene

ENSEMBL:
Gene Tree for ELL3 (if available)
TreeFam:
Gene Tree for ELL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ELL3: view image

Paralogs for ELL3 Gene

Paralogs for ELL3 Gene

(1) SIMAP similar genes for ELL3 Gene using alignment to 2 proteins:

  • ELL3_HUMAN
  • C9JHD8_HUMAN
genes like me logo Genes that share paralogs with ELL3: view

Variants for ELL3 Gene

Sequence variations from dbSNP and Humsavar for ELL3 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000521898 -- 43,776,887(-) C/G coding_sequence_variant, missense_variant
rs1000849516 -- 43,778,702(-) C/A/T upstream_transcript_variant
rs1000977658 -- 43,777,190(-) AGAG/AG 5_prime_UTR_variant
rs1000991580 -- 43,778,880(-) C/T upstream_transcript_variant
rs1001486755 -- 43,775,202(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ELL3 Gene

Variant ID Type Subtype PubMed ID
esv2760028 CNV gain+loss 17122850
nsv1036318 CNV gain 25217958

Variation tolerance for ELL3 Gene

Residual Variation Intolerance Score: 53.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.79; 73.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ELL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ELL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ELL3 Gene

Disorders for ELL3 Gene

Additional Disease Information for ELL3

No disorders were found for ELL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ELL3 Gene

Publications for ELL3 Gene

  1. Identification, cloning, expression, and biochemical characterization of the testis-specific RNA polymerase II elongation factor ELL3. (PMID: 10882741) Miller T … Shilatifard A (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. The little elongation complex regulates small nuclear RNA transcription. (PMID: 22195968) Smith ER … Shilatifard A (Molecular cell 2011) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for ELL3 Gene

Sources for ELL3 Gene

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