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 euka... See more...

Aliases for SECISBP2 Gene

Aliases for SECISBP2 Gene

  • SECIS Binding Protein 2 2 3 5
  • Selenocysteine Insertion Sequence-Binding Protein 2 2 3 4
  • Sec Insertion Sequence-Binding Protein 2 2 3
  • SBP2 3 4
  • 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 Viral mRNA Translation and Selenium Metabolism and Selenoproteins. Gene Ontology (GO) annotations related to this gene include ribonucleoprotein complex binding. An important paralog of this gene is SECISBP2L.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for SECISBP2 Gene

Genomics for SECISBP2 Gene

GeneHancer (GH) Regulatory Elements for SECISBP2 Gene

Promoters and enhancers for SECISBP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J089316 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 813.6 +0.3 258 4 PPP1R10 E2F8 SIN3A SP1 ZBTB40 CTCF SREBF1 SIX5 FOXA1 RBPJ SECISBP2 lnc-SEMA4D-9 SEMA4D CKS2 piR-32064
GH09J089309 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 31.4 -6.2 -6166 6.4 ZNF24 ZBTB40 SP1 SREBF1 POLR2A USF2 ATF1 FOS CREB1 HCFC1 CKS2 MIR3153 LOC105376136 NONHSAG052777.2 lnc-SEMA4D-4 SHC3 SECISBP2 SEMA4D lnc-SEMA4D-9
GH09J089495 Promoter/Enhancer 1.8 EPDnew ENCODE CraniofacialAtlas dbSUPER 25.5 +179.8 179750 4.5 ZNF701 NKRF POLR2A MLLT1 ZNF687 PRDM1 CREM MTA1 IKZF1 GLIS2 SEMA4D SECISBP2 piR-44878-061 lnc-SEMA4D-5
GH09J089518 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 24.9 +204.4 204449 9.2 SP1 ETV6 RELA POLR2A MLLT1 ZNF687 PRDM1 CREM ZNF639 IKZF1 SECISBP2 SEMA4D SHC3 LOC105376137 piR-44878-061 lnc-SEMA4D-5
GH09J089922 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas 25.5 +604.9 604926 2.4 FOXA1 MLX TCF7L2 NR2F1 NR2F6 RAD21 ELF3 SP1 TFE3 ZNF384 HSALNG0072627 SECISBP2 CKS2 GADD45G HSALNG0072626 ENSG00000237626
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SECISBP2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SECISBP2 gene promoter:
  • AP-4
  • c-Myc
  • CREB
  • deltaCREB
  • FOXD3
  • FOXO1
  • FOXO1a
  • Max
  • Pbx1a
  • YY1

Genomic Locations for SECISBP2 Gene

Genomic Locations for SECISBP2 Gene
chr9:89,318,473-89,367,117
(GRCh38/hg38)
Size:
48,645 bases
Orientation:
Plus strand
chr9:91,933,412-91,974,561
(GRCh37/hg19)
Size:
41,150 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

Suggested Antigen Peptide Sequences for SECISBP2 Gene

GenScript: Design optimal peptide antigens:
  • SECISBP2 protein (A4FTX8_HUMAN)
  • SECIS binding protein 2 (Q5HYY5_HUMAN)
  • SBP2 protein (Q7L1Z0_HUMAN)
  • Selenocysteine insertion sequence-binding protein 2 (SEBP2_HUMAN)
genes like me logo Genes that share domains with SECISBP2: view

No data available for Graphical View of Domain Structure and 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 HDA,IEA 22658674
GO:0003730 mRNA 3'-UTR binding IDA 16962588
GO:0005515 protein binding IPI 25416956
GO:0035368 selenocysteine insertion sequence binding IBA 21873635
GO:0043021 ribonucleoprotein complex binding IBA 21873635
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SECISBP2

Clone Products

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 4
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:1990904 ribonucleoprotein complex IBA 21873635
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 21873635
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SECISBP2

Clone Products

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, 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)
  • Liver(2)

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

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • skeleton
Regions:
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

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 32
  • 99.53 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SECISBP2 33 32
  • 83.83 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SECISBP2 33 32
  • 81.3 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Secisbp2 32
  • 78.98 (n)
mouse
(Mus musculus)
Mammalia Secisbp2 17 33 32
  • 77.92 (n)
oppossum
(Monodelphis domestica)
Mammalia SECISBP2 33
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves SECISBP2 33 32
  • 58 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SECISBP2 33
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia secisbp2 32
  • 60.73 (n)
Str.18761 32
zebrafish
(Danio rerio)
Actinopterygii LOC101883890 32
  • 57.9 (n)
secisbp2 33
  • 42 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4041 32
fruit fly
(Drosophila melanogaster)
Insecta Sbp2 33
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SECISBP2: view image

Paralogs for SECISBP2 Gene

Paralogs for SECISBP2 Gene

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

  • SEBP2_HUMAN
  • A4FTX8_HUMAN
  • F8W892_HUMAN
  • Q4V370_HUMAN
  • Q5HYY5_HUMAN

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 Variation AA Info Type
rs119461976 pathogenic, Thyroid hormone metabolism, abnormal, Abnormal thyroid hormone metabolism (ATHYHM) [MIM:609698] 89,348,095(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs119461977 pathogenic, Thyroid hormone metabolism, abnormal 89,341,356(+) A/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs730880269 pathogenic, Thyroid hormone metabolism, abnormal 89,338,609(+) G/A intron_variant
rs1554716257 likely-pathogenic, not provided 89,325,526(+) TT/T 5_prime_UTR_variant, coding_sequence_variant, frameshift, intron_variant, non_coding_transcript_variant
rs764344701 likely-pathogenic, not provided 89,328,674(+) C/T 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, stop_gained

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)

Additional Variant Information 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, GTR, Orphanet, DISEASES, and GeneCards

- 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.

Additional Disease Information for SECISBP2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 23 56
  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 56
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 43 56
  4. Genetic variants in selenoprotein genes increase risk of colorectal cancer. (PMID: 20378690) Méplan C … Hesketh JE (Carcinogenesis 2010) 3 43 56
  5. Known turnover and translation regulatory RNA-binding proteins interact with the 3' UTR of SECIS-binding protein 2. (PMID: 19106619) Bubenik JL … Driscoll DM (RNA biology 2009) 3 23 56

Products for SECISBP2 Gene

Sources for SECISBP2 Gene