Human Gene SLFN13 (uc002hjm.2)
  Description: Homo sapiens schlafen family member 13 (SLFN13), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:33,762,115-33,775,856 Size: 13,742 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr17:33,767,614-33,771,706 Size: 4,093 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:33,762,115-33,775,856)mRNA (may differ from genome)Protein (566 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtPubMed
TreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SLN13_HUMAN
DESCRIPTION: RecName: Full=Schlafen family member 13;
SIMILARITY: Belongs to the Schlafen family.
SEQUENCE CAUTION: Sequence=AK127728; Type=Frameshift; Positions=261;

-  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: 13.39 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 73.93 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 -190.20598-0.318 Picture PostScript Text
3' UTR -1611.725499-0.293 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
IPR007421 - ATPase_AAA-4
IPR018647 - DUF2075

Pfam Domains:
PF09848 - Uncharacterized conserved protein (DUF2075)

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q68D06
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005524 ATP binding

Cellular Component:
GO:0005622 intracellular


-  Descriptions from all associated GenBank mRNAs
  CR749630 - Homo sapiens mRNA; cDNA DKFZp686I026 (from clone DKFZp686I026).
LF384780 - JP 2014500723-A/192283: Polycomb-Associated Non-Coding RNAs.
JD147076 - Sequence 128100 from Patent EP1572962.
BC171771 - Homo sapiens schlafen family member 13, mRNA (cDNA clone MGC:198486 IMAGE:9054425), complete cds.
BC136622 - Homo sapiens schlafen family member 13, mRNA (cDNA clone MGC:168235 IMAGE:9020612), complete cds.
AK074465 - Homo sapiens cDNA FLJ23885 fis, clone LNG13907.
AL833747 - Homo sapiens mRNA; cDNA DKFZp666J196 (from clone DKFZp666J196).
AL832726 - Homo sapiens mRNA; cDNA DKFZp313N099 (from clone DKFZp313N099).
AK122750 - Homo sapiens cDNA FLJ16277 fis, clone NT2RI3000423, highly similar to Homo sapiens likley ortholog of mouse schlafen 10, mRNA.
JD355868 - Sequence 336892 from Patent EP1572962.
JD343692 - Sequence 324716 from Patent EP1572962.
JD184704 - Sequence 165728 from Patent EP1572962.
JD343077 - Sequence 324101 from Patent EP1572962.
JD349316 - Sequence 330340 from Patent EP1572962.
AK056514 - Homo sapiens cDNA FLJ31952 fis, clone NT2RP7007221, weakly similar to Rattus norvegicus schlafen-4 (SLFN-4) mRNA.
AK127728 - Homo sapiens cDNA FLJ45828 fis, clone NT2RP8005546.
AK126184 - Homo sapiens cDNA FLJ44196 fis, clone THYMU3000133, highly similar to Homo sapiens likley ortholog of mouse schlafen 10, mRNA.
JD085247 - Sequence 66271 from Patent EP1572962.
JD447752 - Sequence 428776 from Patent EP1572962.
JD332062 - Sequence 313086 from Patent EP1572962.
JD175753 - Sequence 156777 from Patent EP1572962.
JD430680 - Sequence 411704 from Patent EP1572962.
JD472270 - Sequence 453294 from Patent EP1572962.
JD294062 - Sequence 275086 from Patent EP1572962.
JD327184 - Sequence 308208 from Patent EP1572962.
JD455130 - Sequence 436154 from Patent EP1572962.
JD269031 - Sequence 250055 from Patent EP1572962.
JD221916 - Sequence 202940 from Patent EP1572962.
JD546317 - Sequence 527341 from Patent EP1572962.
JD083121 - Sequence 64145 from Patent EP1572962.
JD238477 - Sequence 219501 from Patent EP1572962.
JD311230 - Sequence 292254 from Patent EP1572962.
JD097678 - Sequence 78702 from Patent EP1572962.
JD512755 - Sequence 493779 from Patent EP1572962.
JD412787 - Sequence 393811 from Patent EP1572962.
JD197807 - Sequence 178831 from Patent EP1572962.
JD135924 - Sequence 116948 from Patent EP1572962.
JD504860 - Sequence 485884 from Patent EP1572962.
JD248457 - Sequence 229481 from Patent EP1572962.
JD162693 - Sequence 143717 from Patent EP1572962.
JD082668 - Sequence 63692 from Patent EP1572962.
JD082669 - Sequence 63693 from Patent EP1572962.
JD073105 - Sequence 54129 from Patent EP1572962.
JD439680 - Sequence 420704 from Patent EP1572962.
JD540668 - Sequence 521692 from Patent EP1572962.
AM392937 - Synthetic construct Homo sapiens clone IMAGE:100002230 for hypothetical protein (SLFN13 gene).
LF327035 - JP 2014500723-A/134538: Polycomb-Associated Non-Coding RNAs.
JD111236 - Sequence 92260 from Patent EP1572962.
JD423473 - Sequence 404497 from Patent EP1572962.
JD315647 - Sequence 296671 from Patent EP1572962.
JD201392 - Sequence 182416 from Patent EP1572962.
MA620357 - JP 2018138019-A/192283: Polycomb-Associated Non-Coding RNAs.
MA562612 - JP 2018138019-A/134538: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK122750, E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81, SLN13_HUMAN
UCSC ID: uc002hjm.2
RefSeq Accession: NM_144682
Protein: Q68D06 (aka SLN13_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK122750.1
exon count: 7CDS single in 3' UTR: no RNA size: 3910
ORF size: 1701CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3280.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.