Human Gene SECISBP2 (uc011ltk.1)
  Description: Homo sapiens SECIS binding protein 2 (SECISBP2), mRNA.
RefSeq Summary (NM_024077): The protein encoded by this gene is one of the essential components of the machinery involved in co-translational insertion of selenocysteine (Sec) into selenoproteins. Sec is encoded by the UGA codon, which normally signals translation termination. The recoding of UGA as Sec codon requires a Sec insertion sequence (SECIS) element; present in the 3' untranslated regions of eukaryotic selenoprotein mRNAs. This protein specifically binds to the SECIS element, which is stimulated by a Sec-specific translation elongation factor. Mutations in this gene have been associated with reduction in enzymatic activity of type II iodothyronine deiodinase (a selenoprotein) and abnormal thyroid hormone metabolism. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017].
Transcript (Including UTRs)
   Position: hg19 chr9:91,933,412-91,974,561 Size: 41,150 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr9:91,933,492-91,973,739 Size: 40,248 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:91,933,412-91,974,561)mRNA (may differ from genome)Protein (853 aa)
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MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SEBP2_HUMAN
DESCRIPTION: RecName: Full=Selenocysteine insertion sequence-binding protein 2; Short=SECIS-binding protein 2;
FUNCTION: Binds to the SECIS element in the 3'-UTR of some mRNAs encoding selenoproteins. Binding is stimulated by SELB.
SUBUNIT: Interacts with SELB (By similarity).
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Expressed at high levels in testis.
DISEASE: Defects in SECISBP2 are a cause of abnormal thyroid hormone metabolism (ATHYHM) [MIM:609698]. This phenotype is associated with a reduction in type II iodothyronine deiodinase activity.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SECISBP2
CDC HuGE Published Literature: SECISBP2

-  MalaCards Disease Associations
  MalaCards Gene Search: SECISBP2
Diseases sorted by gene-association score: thyroid hormone metabolism, abnormal* (1650), pontocerebellar hypoplasia type 2d (12), muscular dystrophy, rigid spine, 1 (4)
* = Manually curated disease association

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

+  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: 19.23 RPKM in Testis
Total median expression: 404.49 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 -33.5080-0.419 Picture PostScript Text
3' UTR -258.50822-0.314 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
IPR004038 - Ribosomal_L7Ae/L30e/S12e/Gad45

Pfam Domains:
PF01248 - Ribosomal protein L7Ae/L30e/S12e/Gadd45 family

SCOP Domains:
55315 - L30e-like

ModBase Predicted Comparative 3D Structure on Q96T21
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0035368 selenocysteine insertion sequence binding
GO:0043021 ribonucleoprotein complex binding

Biological Process:
GO:0001514 selenocysteine incorporation
GO:0006412 translation
GO:0021756 striatum development
GO:0048666 neuron development
GO:2000623 negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AK302852 - Homo sapiens cDNA FLJ54472 complete cds, highly similar to SECIS-binding protein 2.
KX533480 - Homo sapiens selenocysteine insertion sequence-binding protein 2 (SECISBP2) mRNA, complete cds.
AK090608 - Homo sapiens cDNA FLJ33289 fis, clone BGGI12001075, moderately similar to Rattus norvegicus mRNA for SECIS binding protein 2 (sbp2 gene).
AX746532 - Sequence 57 from Patent EP1308459.
AK290182 - Homo sapiens cDNA FLJ75613 complete cds.
BC036109 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone MGC:33935 IMAGE:5296292), complete cds.
AB208940 - Homo sapiens premature mRNA for hypothetical protein DKFZp434B216 variant.
BC001189 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone IMAGE:3354449), complete cds.
AL136881 - Homo sapiens mRNA; cDNA DKFZp434B216 (from clone DKFZp434B216).
AF380995 - Homo sapiens SECIS binding protein 2 (SBP2) mRNA, complete cds.
BC099900 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone IMAGE:6146359), partial cds.
BC068466 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone IMAGE:5297396).
KJ903142 - Synthetic construct Homo sapiens clone ccsbBroadEn_12536 SECISBP2 gene, encodes complete protein.
AK299161 - Homo sapiens cDNA FLJ61343 complete cds, highly similar to SECIS-binding protein 2.
AB463244 - Synthetic construct DNA, clone: pF1KB8574, Homo sapiens SECISBP2 gene for SECIS binding protein 2, without stop codon, in Flexi system.
AM392812 - Synthetic construct Homo sapiens clone IMAGE:100001851 for hypothetical protein (SECISBP2 gene).
AM393701 - Synthetic construct Homo sapiens clone IMAGE:100002025 for hypothetical protein (SECISBP2 gene).
BX648787 - Homo sapiens mRNA; cDNA DKFZp686C09169 (from clone DKFZp686C09169).
BC023142 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone IMAGE:3917564), partial cds.
AK023078 - Homo sapiens cDNA FLJ13016 fis, clone NT2RP3000624, moderately similar to Rattus norvegicus mRNA for SECIS binding protein 2 (sbp2 gene).
BC038854 - Homo sapiens SECIS binding protein 2, mRNA (cDNA clone IMAGE:5209694), **** WARNING: chimeric clone ****.
JD315710 - Sequence 296734 from Patent EP1572962.
JD087604 - Sequence 68628 from Patent EP1572962.
JD109300 - Sequence 90324 from Patent EP1572962.
JD344457 - Sequence 325481 from Patent EP1572962.
JD448760 - Sequence 429784 from Patent EP1572962.
JD028179 - Sequence 9203 from Patent EP1572962.
JD561081 - Sequence 542105 from Patent EP1572962.
JD349177 - Sequence 330201 from Patent EP1572962.
JD177581 - Sequence 158605 from Patent EP1572962.
JD266839 - Sequence 247863 from Patent EP1572962.
JD465925 - Sequence 446949 from Patent EP1572962.
JD232368 - Sequence 213392 from Patent EP1572962.
JD279844 - Sequence 260868 from Patent EP1572962.
JD553919 - Sequence 534943 from Patent EP1572962.
JD303340 - Sequence 284364 from Patent EP1572962.
JD314413 - Sequence 295437 from Patent EP1572962.
JD244765 - Sequence 225789 from Patent EP1572962.
JD439196 - Sequence 420220 from Patent EP1572962.

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

Protein Q96T21 (Reactome details) participates in the following event(s):

R-HSA-2408529 Sec-tRNA(Sec):EEFSEC:GTP binds to 80S Ribosome
R-HSA-5333615 80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC
R-HSA-2408557 Selenocysteine synthesis
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: AK302852, NM_024077, NP_076982, Q5HYY1, Q8IYC0, Q96T21, Q9H0A1, SBP2, SEBP2_HUMAN
UCSC ID: uc011ltk.1
RefSeq Accession: NM_024077
Protein: Q96T21 (aka SEBP2_HUMAN or SIB2_HUMAN)
CCDS: CCDS6683.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK302852.1
exon count: 17CDS single in 3' UTR: no RNA size: 2888
ORF size: 2562CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 5324.00frame shift in genome: no % Coverage: 99.24
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.