Human Gene ELL3 (ENST00000319359.8) from GENCODE V44
  Description: Homo sapiens elongation factor for RNA polymerase II 3 (ELL3), mRNA. (from RefSeq NM_025165)
Gencode Transcript: ENST00000319359.8
Gencode Gene: ENSG00000128886.12
Transcript (Including UTRs)
   Position: hg38 chr15:43,772,620-43,776,966 Size: 4,347 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr15:43,773,116-43,776,901 Size: 3,786 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:43,772,620-43,776,966)mRNA (may differ from genome)Protein (397 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ELL3_HUMAN
DESCRIPTION: RecName: Full=RNA polymerase II elongation factor ELL3;
FUNCTION: Elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Testis specific.
SIMILARITY: Belongs to the ELL/occludin family.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.00 RPKM in Adipose - Subcutaneous
Total median expression: 0.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -25.4065-0.391 Picture PostScript Text
3' UTR -124.50496-0.251 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010844 - Occludin_RNApol2_elong_fac_ELL
IPR019464 - RNA_pol_II_elong_fac_ELL

Pfam Domains:
PF10390 - RNA polymerase II elongation factor ELL
PF07303 - Occludin homology domain

ModBase Predicted Comparative 3D Structure on Q9HB65
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0035326 enhancer binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006354 DNA-templated transcription, elongation
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0007283 spermatogenesis
GO:0010717 regulation of epithelial to mesenchymal transition
GO:0032786 positive regulation of DNA-templated transcription, elongation
GO:0042795 snRNA transcription from RNA polymerase II promoter
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048863 stem cell differentiation
GO:0050769 positive regulation of neurogenesis
GO:1901797 negative regulation of signal transduction by p53 class mediator
GO:1902166 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:2000179 positive regulation of neural precursor cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0008023 transcription elongation factor complex


-  Descriptions from all associated GenBank mRNAs
  HQ447725 - Synthetic construct Homo sapiens clone IMAGE:100071056; CCSB012411_01 elongation factor RNA polymerase II-like 3 (ELL3) gene, encodes complete protein.
KJ894800 - Synthetic construct Homo sapiens clone ccsbBroadEn_04194 ELL3 gene, encodes complete protein.
AK093233 - Homo sapiens cDNA FLJ35914 fis, clone TESTI2010354, highly similar to Homo sapiens RNA polymerase II elongation factor ELL3 mRNA.
LF205860 - JP 2014500723-A/13363: Polycomb-Associated Non-Coding RNAs.
MA441437 - JP 2018138019-A/13363: Polycomb-Associated Non-Coding RNAs.
AK057528 - Homo sapiens cDNA FLJ32966 fis, clone TESTI2008699, highly similar to RNA polymerase II elongation factor ELL3.
AK126384 - Homo sapiens cDNA FLJ44420 fis, clone UTERU2002198, highly similar to RNA polymerase II elongation factor ELL3.
BC006548 - Homo sapiens elongation factor RNA polymerase II-like 3, mRNA (cDNA clone MGC:2443 IMAGE:2821972), complete cds.
BC019293 - Homo sapiens elongation factor RNA polymerase II-like 3, mRNA (cDNA clone MGC:4106 IMAGE:2821972), complete cds.
AK026290 - Homo sapiens cDNA: FLJ22637 fis, clone HSI06677.
JD085038 - Sequence 66062 from Patent EP1572962.
JD279838 - Sequence 260862 from Patent EP1572962.
JD345443 - Sequence 326467 from Patent EP1572962.
AF276512 - Homo sapiens RNA polymerase II elongation factor ELL3 mRNA, partial cds.
CR457358 - Homo sapiens full open reading frame cDNA clone RZPDo834G1113D for gene ELL3, elongation factor RNA polymerase II-like 3; complete cds, incl. stopcodon.
LF349028 - JP 2014500723-A/156531: Polycomb-Associated Non-Coding RNAs.
MA584605 - JP 2018138019-A/156531: Polycomb-Associated Non-Coding RNAs.
CU675445 - Synthetic construct Homo sapiens gateway clone IMAGE:100021915 5' read ELL3 mRNA.
LF349030 - JP 2014500723-A/156533: Polycomb-Associated Non-Coding RNAs.
MA584607 - JP 2018138019-A/156533: Polycomb-Associated Non-Coding RNAs.
JD417292 - Sequence 398316 from Patent EP1572962.
JD392387 - Sequence 373411 from Patent EP1572962.
JD036931 - Sequence 17955 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9HB65 (Reactome details) participates in the following event(s):

R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-HSA-6807505 RNA polymerase II transcribes snRNA genes
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ELL3_HUMAN, ENST00000319359.1, ENST00000319359.2, ENST00000319359.3, ENST00000319359.4, ENST00000319359.5, ENST00000319359.6, ENST00000319359.7, NM_025165, Q6I9Z7, Q9H634, Q9HB65, uc001zsw.1, uc001zsw.2, uc001zsw.3
UCSC ID: ENST00000319359.8
RefSeq Accession: NM_025165
Protein: Q9HB65 (aka ELL3_HUMAN)
CCDS: CCDS10102.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.