Human Gene ALYREF (ENST00000505490.3_7) from GENCODE V47lift37
  Description: Aly/REF export factor, transcript variant 2 (from RefSeq NR_158770.1)
Gencode Transcript: ENST00000505490.3_7
Gencode Gene: ENSG00000183684.8_9
Transcript (Including UTRs)
   Position: hg19 chr17:79,845,711-79,849,462 Size: 3,752 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr17:79,846,007-79,849,456 Size: 3,450 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:79,845,711-79,849,462)mRNA (may differ from genome)Protein (264 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PB61_HUMAN
DESCRIPTION: SubName: Full=THO complex subunit 4;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 63.92 RPKM in Testis
Total median expression: 1017.17 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -88.00296-0.297 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
IPR025715 - FoP_duplication
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13865 - C-terminal duplication domain of Friend of PRMT1
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on E9PB61
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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
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Cellular Component:
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AF086513 - Homo sapiens full length insert cDNA clone ZE03B06.
BC052302 - Homo sapiens THO complex 4, mRNA (cDNA clone MGC:59943 IMAGE:6381528), complete cds.
AF047002 - Homo sapiens transcriptional coactivator ALY mRNA, partial cds.
JD427399 - Sequence 408423 from Patent EP1572962.
JD388698 - Sequence 369722 from Patent EP1572962.
EU831428 - Synthetic construct Homo sapiens clone HAIB:100066457; DKFZo008C0317 THO complex 4 protein (THOC4) gene, encodes complete protein.
EU831521 - Synthetic construct Homo sapiens clone HAIB:100066550; DKFZo004C0318 THO complex 4 protein (THOC4) gene, encodes complete protein.
DQ583375 - Homo sapiens piRNA piR-50487, complete sequence.
DQ578942 - Homo sapiens piRNA piR-47054, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: ALYREF , E9PB61, E9PB61_HUMAN, ENST00000505490.1, ENST00000505490.2, NR_158770, uc322zvp.1, uc322zvp.2
UCSC ID: ENST00000505490.3_7
RefSeq Accession: NM_005782.4
Protein: E9PB61

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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