Human Gene TRERF1 (ENST00000695948.1_5) from GENCODE V47lift37
  Description: transcriptional regulating factor 1, transcript variant 5 (from RefSeq NM_001395490.1)
Gencode Transcript: ENST00000695948.1_5
Gencode Gene: ENSG00000124496.13_15
Transcript (Including UTRs)
   Position: hg19 chr6:42,192,669-42,419,664 Size: 226,996 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr6:42,196,083-42,237,328 Size: 41,246 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:42,192,669-42,419,664)mRNA (may differ from genome)Protein (1212 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedUniProtKBWikipedia

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: TRERF1
Diseases sorted by gene-association score: swayback (13), estrogen resistance (12)

-  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.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -302.90791-0.383 Picture PostScript Text
3' UTR -908.303414-0.266 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.

-  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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Descriptions from all associated GenBank mRNAs
  AM404182 - Homo sapiens mRNA for breast cancer anti-estrogen resistance 2 (BCAR2 gene), isoform alpha.
AM404183 - Homo sapiens mRNA for breast cancer anti-estrogen resistance 2 (BCAR2 gene), isoform beta, from the beta long transcript.
AK002096 - Homo sapiens cDNA FLJ11234 fis, clone PLACE1008465.
AF297872 - Homo sapiens zinc finger transcription factor TReP-132 mRNA, complete cds.
AK127493 - Homo sapiens cDNA FLJ45586 fis, clone BRTHA3014000, highly similar to Transcriptional-regulating factor 1.
AM404259 - Homo sapiens mRNA for breast cancer anti-estrogen resistance 2 (BCAR2 gene), isoform beta, from the beta short transcript.
AJ277275 - Homo sapiens mRNA for rapa-1 (rapa gene).
AJ277276 - Homo sapiens mRNA for rapa-2 (rapa gene).
BC156203 - Synthetic construct Homo sapiens clone IMAGE:100061587, MGC:190040 transcriptional regulating factor 1 (TRERF1) mRNA, encodes complete protein.
AB384805 - Synthetic construct DNA, clone: pF1KB3458, Homo sapiens TRERF1 gene for transcriptional-regulating factor 1, complete cds, without stop codon, in Flexi system.
AK308473 - Homo sapiens cDNA, FLJ98514.
LF210874 - JP 2014500723-A/18377: Polycomb-Associated Non-Coding RNAs.
LF341666 - JP 2014500723-A/149169: Polycomb-Associated Non-Coding RNAs.
AF111801 - Homo sapiens MSTP020 (MST020) mRNA, complete cds.
LF341665 - JP 2014500723-A/149168: Polycomb-Associated Non-Coding RNAs.
DQ574983 - Homo sapiens piRNA piR-43095, complete sequence.
BC047920 - Homo sapiens, clone IMAGE:6192478, mRNA.
JD250334 - Sequence 231358 from Patent EP1572962.
JD163154 - Sequence 144178 from Patent EP1572962.
MA577243 - JP 2018138019-A/149169: Polycomb-Associated Non-Coding RNAs.
MA577242 - JP 2018138019-A/149168: Polycomb-Associated Non-Coding RNAs.
MA446451 - JP 2018138019-A/18377: Polycomb-Associated Non-Coding RNAs.
JD037069 - Sequence 18093 from Patent EP1572962.
JD232789 - Sequence 213813 from Patent EP1572962.
JD470461 - Sequence 451485 from Patent EP1572962.
JD111986 - Sequence 93010 from Patent EP1572962.
JD096831 - Sequence 77855 from Patent EP1572962.
JD290281 - Sequence 271305 from Patent EP1572962.
JD505521 - Sequence 486545 from Patent EP1572962.
JD525770 - Sequence 506794 from Patent EP1572962.
JD190934 - Sequence 171958 from Patent EP1572962.
JD372701 - Sequence 353725 from Patent EP1572962.
JD075810 - Sequence 56834 from Patent EP1572962.
JD092227 - Sequence 73251 from Patent EP1572962.
JD290240 - Sequence 271264 from Patent EP1572962.
JD206597 - Sequence 187621 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A8Q3SI57, A0A8Q3SI57_HUMAN, NM_001395490, TRERF1 , uc331ago.1, uc331ago.2
UCSC ID: ENST00000695948.1_5
RefSeq Accession: NM_001395490.1

-  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.