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Aliases for SECISBP2 Gene

Aliases for SECISBP2 Gene

  • SECIS Binding Protein 2 2 3 5
  • Sec Insertion Sequence-Binding Protein 2 2 3
  • SBP2 3 4
  • Selenocysteine Insertion Sequence-Binding Protein 2 3
  • SECIS-Binding Protein 2 4

External Ids for SECISBP2 Gene

Previous GeneCards Identifiers for SECISBP2 Gene

  • GC09P087423
  • GC09P089162
  • GC09P091123
  • GC09P091933
  • GC09P061766

Summaries for SECISBP2 Gene

Entrez Gene Summary for SECISBP2 Gene

  • 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]

GeneCards Summary for SECISBP2 Gene

SECISBP2 (SECIS Binding Protein 2) is a Protein Coding gene. Diseases associated with SECISBP2 include Thyroid Hormone Metabolism, Abnormal and Pontocerebellar Hypoplasia Type 2D. Among its related pathways are Metabolism and Selenium Metabolism and Selenoproteins. GO annotations related to this gene include poly(A) RNA binding and ribonucleoprotein complex binding. An important paralog of this gene is SECISBP2L.

UniProtKB/Swiss-Prot for SECISBP2 Gene

  • Binds to the SECIS element in the 3-UTR of some mRNAs encoding selenoproteins. Binding is stimulated by SELB.

Gene Wiki entry for SECISBP2 Gene

Additional gene information for SECISBP2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SECISBP2 Gene

Genomics for SECISBP2 Gene

Regulatory Elements for SECISBP2 Gene

Enhancers for SECISBP2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H089518 1.8 FANTOM5 Ensembl ENCODE dbSUPER 24.9 +204.6 204600 9 HDGF PKNOX1 TBL1XR1 RB1 SIN3A BATF BRCA1 RFX5 SMARCC2 RCOR1 SECISBP2 SEMA4D SHC3 LOC105376137
GH09H089316 1.1 ENCODE 35.9 +0.3 259 4 PKNOX1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SECISBP2 SEMA4D CKS2 PIR43063
GH09H089399 1.5 FANTOM5 Ensembl ENCODE dbSUPER 16.4 +82.5 82459 2 ZNF687 TBL1XR1 ELF1 EBF1 IKZF1 NBN RUNX3 CREM IKZF2 CHD2 SECISBP2 SEMA4D PA2G4P6 PIR43063
GH09H089405 1.3 Ensembl ENCODE dbSUPER 14.6 +90.0 90041 6 SIN3A BATF RAD21 ZNF143 ZNF207 ATF7 ETV6 RUNX3 CREM IKZF2 SEMA4D SECISBP2 PA2G4P6 PIR43063
GH09H089659 1.4 Ensembl ENCODE dbSUPER 13.1 +344.4 344385 6 FOXA2 PKNOX1 NFIB ZFP64 RAD21 YY1 FOS NFYC ELF1 REST SECISBP2 GADD45G LOC102724237 UNQ6494
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SECISBP2 on UCSC Golden Path with GeneCards custom track

Promoters for SECISBP2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000237493 327 1601 PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 ZNF207

Genomic Location for SECISBP2 Gene

Chromosome:
9
Start:
89,318,473 bp from pter
End:
89,367,117 bp from pter
Size:
48,645 bases
Orientation:
Plus strand

Genomic View for SECISBP2 Gene

Genes around SECISBP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SECISBP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SECISBP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SECISBP2 Gene

Proteins for SECISBP2 Gene

  • Protein details for SECISBP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96T21-SEBP2_HUMAN
    Recommended name:
    Selenocysteine insertion sequence-binding protein 2
    Protein Accession:
    Q96T21
    Secondary Accessions:
    • F8W892
    • Q5HYY1
    • Q7L1Z0
    • Q8IYC0
    • Q9H0A1

    Protein attributes for SECISBP2 Gene

    Size:
    854 amino acids
    Molecular mass:
    95462 Da
    Quaternary structure:
    • Interacts with SELB.

    Alternative splice isoforms for SECISBP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SECISBP2 Gene

Post-translational modifications for SECISBP2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SECISBP2 Gene

Domains & Families for SECISBP2 Gene

Gene Families for SECISBP2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SECISBP2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SECISBP2: view

No data available for UniProtKB/Swiss-Prot for SECISBP2 Gene

Function for SECISBP2 Gene

Molecular function for SECISBP2 Gene

UniProtKB/Swiss-Prot Function:
Binds to the SECIS element in the 3-UTR of some mRNAs encoding selenoproteins. Binding is stimulated by SELB.

Phenotypes From GWAS Catalog for SECISBP2 Gene

Gene Ontology (GO) - Molecular Function for SECISBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 22658674
GO:0003730 mRNA 3-UTR binding IDA 16962588
GO:0005515 protein binding IPI 25416956
GO:0035368 selenocysteine insertion sequence binding IBA --
GO:0043021 ribonucleoprotein complex binding IBA --
genes like me logo Genes that share ontologies with SECISBP2: view
genes like me logo Genes that share phenotypes with SECISBP2: view

Human Phenotype Ontology for SECISBP2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SECISBP2 Gene

MGI Knock Outs for SECISBP2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SECISBP2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SECISBP2 Gene

Localization for SECISBP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SECISBP2 Gene

Isoform 1: Nucleus.
Isoform 2: Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SECISBP2 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SECISBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005739 mitochondrion IEA --
GO:0030529 intracellular ribonucleoprotein complex IBA --
genes like me logo Genes that share ontologies with SECISBP2: view

Pathways & Interactions for SECISBP2 Gene

genes like me logo Genes that share pathways with SECISBP2: view

Pathways by source for SECISBP2 Gene

Gene Ontology (GO) - Biological Process for SECISBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001514 selenocysteine incorporation IBA --
GO:0006412 translation IEA --
GO:0021756 striatum development IEA --
GO:0048666 neuron development IEA --
GO:2000623 negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA --
genes like me logo Genes that share ontologies with SECISBP2: view

No data available for SIGNOR curated interactions for SECISBP2 Gene

Drugs & Compounds for SECISBP2 Gene

(1) Drugs for SECISBP2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for SECISBP2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SECISBP2: view

Transcripts for SECISBP2 Gene

Unigene Clusters for SECISBP2 Gene

SECIS binding protein 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SECISBP2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SECISBP2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^
SP1:
SP2: - - -
SP3:
SP4: -
SP5: -
SP6:
SP7: -
SP8: -
SP9:
SP10:
SP11: - - - - -
SP12: - - - -

ExUns: 18a · 18b ^ 19 ^ 20
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for SECISBP2 Gene

GeneLoc Exon Structure for
SECISBP2
ECgene alternative splicing isoforms for
SECISBP2

Expression for SECISBP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SECISBP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SECISBP2 Gene

This gene is overexpressed in Testis (27.9), Pancreatic juice (13.2), and Fetal ovary (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SECISBP2 Gene



Protein tissue co-expression partners for SECISBP2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SECISBP2 Gene:

SECISBP2

SOURCE GeneReport for Unigene cluster for SECISBP2 Gene:

Hs.59804

mRNA Expression by UniProt/SwissProt for SECISBP2 Gene:

Q96T21-SEBP2_HUMAN
Tissue specificity: Expressed at high levels in testis.

Evidence on tissue expression from TISSUES for SECISBP2 Gene

  • Nervous system(4.7)
  • Thyroid gland(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SECISBP2 Gene

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • skeleton
Organs:
Head and neck:
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • thyroid
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SECISBP2: view

Primer Products

No data available for mRNA differential expression in normal tissues for SECISBP2 Gene

Orthologs for SECISBP2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SECISBP2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SECISBP2 33 34
  • 99.53 (n)
cow
(Bos Taurus)
Mammalia SECISBP2 33 34
  • 83.83 (n)
dog
(Canis familiaris)
Mammalia SECISBP2 33 34
  • 81.3 (n)
rat
(Rattus norvegicus)
Mammalia Secisbp2 33
  • 78.98 (n)
mouse
(Mus musculus)
Mammalia Secisbp2 33 16 34
  • 77.92 (n)
oppossum
(Monodelphis domestica)
Mammalia SECISBP2 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves SECISBP2 33 34
  • 58 (n)
lizard
(Anolis carolinensis)
Reptilia SECISBP2 34
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia secisbp2 33
  • 60.73 (n)
Str.18761 33
zebrafish
(Danio rerio)
Actinopterygii LOC101883890 33
  • 57.9 (n)
secisbp2 34
  • 42 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4041 33
fruit fly
(Drosophila melanogaster)
Insecta Sbp2 34
  • 27 (a)
OneToMany
Species where no ortholog for SECISBP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SECISBP2 Gene

ENSEMBL:
Gene Tree for SECISBP2 (if available)
TreeFam:
Gene Tree for SECISBP2 (if available)

Paralogs for SECISBP2 Gene

Paralogs for SECISBP2 Gene

(3) SIMAP similar genes for SECISBP2 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for SECISBP2 Gene

genes like me logo Genes that share paralogs with SECISBP2: view

Variants for SECISBP2 Gene

Sequence variations from dbSNP and Humsavar for SECISBP2 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs119461976 Pathogenic, Abnormal thyroid hormone metabolism (ATHYHM) [MIM:609698] 89,348,095(+) AGAAC(A/G)GCAAG nc-transcript-variant, reference, missense
rs119461977 Pathogenic 89,341,356(+) ATTTT(A/T)AAAAT nc-transcript-variant, reference, stop-gained
rs730880269 Pathogenic 89,338,609(+) ATGGT(A/G)TGATA intron-variant
rs1000015045 -- 89,316,645(+) AGTGC(C/T)TGTTT upstream-variant-2KB, utr-variant-3-prime
rs1000020217 -- 89,319,392(+) ACTAT(A/G)TAATC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SECISBP2 Gene

Variant ID Type Subtype PubMed ID
esv29434 CNV gain+loss 19812545
esv3306291 CNV mobile element insertion 20981092
esv3390930 CNV insertion 20981092
esv3621014 CNV gain 21293372
nsv1041327 CNV gain 25217958
nsv831651 CNV gain 17160897

Variation tolerance for SECISBP2 Gene

Residual Variation Intolerance Score: 8.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.79; 58.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SECISBP2 Gene

Human Gene Mutation Database (HGMD)
SECISBP2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SECISBP2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SECISBP2 Gene

Disorders for SECISBP2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SECISBP2 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, and DISEASES

Disorder Aliases PubMed IDs
thyroid hormone metabolism, abnormal
  • short stature-delayed bone age due to thyroid hormone metabolism deficiency
pontocerebellar hypoplasia type 2d
  • progressive cerebello-cerebral atrophy
muscular dystrophy, rigid spine, 1
  • rigid spine muscular dystrophy 1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SEBP2_HUMAN
  • Abnormal thyroid hormone metabolism (ATHYHM) [MIM:609698]: A disorder associated with a reduction in type II iodothyronine deiodinase activity. {ECO:0000269 PubMed:16228000}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SECISBP2

Genetic Association Database (GAD)
SECISBP2
Human Genome Epidemiology (HuGE) Navigator
SECISBP2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SECISBP2
genes like me logo Genes that share disorders with SECISBP2: view

No data available for Genatlas for SECISBP2 Gene

Publications for SECISBP2 Gene

  1. Functional characterization of alternatively spliced human SECISBP2 transcript variants. (PMID: 19004874) Papp LV … Khanna KK (Nucleic acids research 2008) 3 4 22 60
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 60
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  4. Genetic variants in selenoprotein genes increase risk of colorectal cancer. (PMID: 20378690) Méplan C … Hesketh JE (Carcinogenesis 2010) 3 45 60
  5. Clinical and molecular characterization of a novel selenocysteine insertion sequence-binding protein 2 (SBP2) gene mutation (R128X). (PMID: 19602558) Di Cosmo C … Refetoff S (The Journal of clinical endocrinology and metabolism 2009) 3 22 60

Products for SECISBP2 Gene

Sources for SECISBP2 Gene

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