Human Gene SLX4IP (ENST00000334534.10_4) from GENCODE V47lift37
  Description: SLX4 interacting protein (from RefSeq NM_001009608.3)
Gencode Transcript: ENST00000334534.10_4
Gencode Gene: ENSG00000149346.15_8
Transcript (Including UTRs)
   Position: hg19 chr20:10,415,953-10,608,678 Size: 192,726 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr20:10,438,853-10,604,027 Size: 165,175 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:10,415,953-10,608,678)mRNA (may differ from genome)Protein (408 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CT094_HUMAN
DESCRIPTION: RecName: Full=UPF0492 protein C20orf94;
SUBUNIT: Interacts with SLX4/BTBD12; subunit of different structure-specific endonucleases.
INTERACTION: Q8IY92:SLX4; NbExp=4; IntAct=EBI-2370881, EBI-2370740;
SIMILARITY: Belongs to the UPF0492 family.
SEQUENCE CAUTION: Sequence=AAH20787.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH26094.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  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: SLX4IP
Diseases sorted by gene-association score: lymphoblastic leukemia (3)

-  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: 1.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 24.16 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
5' UTR -38.00178-0.213 Picture PostScript Text
3' UTR -1315.104651-0.283 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
  Pfam Domains:
PF15744 - Uncharacterized protein family UPF0492

ModBase Predicted Comparative 3D Structure on Q5VYV7
FrontTopSide
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

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


-  Descriptions from all associated GenBank mRNAs
  LF205923 - JP 2014500723-A/13426: Polycomb-Associated Non-Coding RNAs.
BC020787 - Homo sapiens chromosome 20 open reading frame 94, mRNA (cDNA clone IMAGE:4840139), partial cds.
BC026094 - Homo sapiens chromosome 20 open reading frame 94, mRNA (cDNA clone IMAGE:4807023), partial cds.
MA441500 - JP 2018138019-A/13426: Polycomb-Associated Non-Coding RNAs.
JD312259 - Sequence 293283 from Patent EP1572962.
JD234650 - Sequence 215674 from Patent EP1572962.
LF349711 - JP 2014500723-A/157214: Polycomb-Associated Non-Coding RNAs.
JD335998 - Sequence 317022 from Patent EP1572962.
MA585288 - JP 2018138019-A/157214: Polycomb-Associated Non-Coding RNAs.
LF349738 - JP 2014500723-A/157241: Polycomb-Associated Non-Coding RNAs.
LF349743 - JP 2014500723-A/157246: Polycomb-Associated Non-Coding RNAs.
LF349744 - JP 2014500723-A/157247: Polycomb-Associated Non-Coding RNAs.
LF349745 - JP 2014500723-A/157248: Polycomb-Associated Non-Coding RNAs.
LF349746 - JP 2014500723-A/157249: Polycomb-Associated Non-Coding RNAs.
DQ586877 - Homo sapiens piRNA piR-53989, complete sequence.
MA585315 - JP 2018138019-A/157241: Polycomb-Associated Non-Coding RNAs.
MA585320 - JP 2018138019-A/157246: Polycomb-Associated Non-Coding RNAs.
MA585321 - JP 2018138019-A/157247: Polycomb-Associated Non-Coding RNAs.
MA585322 - JP 2018138019-A/157248: Polycomb-Associated Non-Coding RNAs.
MA585323 - JP 2018138019-A/157249: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf94, ENST00000334534.1, ENST00000334534.2, ENST00000334534.3, ENST00000334534.4, ENST00000334534.5, ENST00000334534.6, ENST00000334534.7, ENST00000334534.8, ENST00000334534.9, NM_001009608, Q05CG2, Q05CT9, Q5VYV7, SLX4I_HUMAN, uc317tzr.1, uc317tzr.2
UCSC ID: ENST00000334534.10_4
RefSeq Accession: NM_001009608.3
Protein: Q5VYV7 (aka CT094_HUMAN)

-  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.