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Aliases for SLBP Gene

Aliases for SLBP Gene

  • Stem-Loop Binding Protein 2 3 5
  • Stem-Loop (Histone) Binding Protein 2 3
  • Histone Binding Protein 2 3
  • HBP 3 4
  • Histone RNA Hairpin-Binding Protein 3
  • Histone Stem-Loop Binding Protein 3
  • Histone Stem-Loop-Binding Protein 4
  • Hairpin Binding Protein, Histone 3

External Ids for SLBP Gene

Previous GeneCards Identifiers for SLBP Gene

  • GC04M001686
  • GC04M001656
  • GC04M001661
  • GC04M001664
  • GC04M001694
  • GC04M001637

Summaries for SLBP Gene

Entrez Gene Summary for SLBP Gene

  • This gene encodes a protein that binds to the stem-loop structure in replication-dependent histone mRNAs. Histone mRNAs do not contain introns or polyadenylation signals, and are processed by endonucleolytic cleavage. The stem-loop structure is essential for efficient processing but this structure also controls the transport, translation and stability of histone mRNAs. Expression of the protein is regulated during the cell cycle, increasing more than 10-fold during the latter part of G1. [provided by RefSeq, Jul 2008]

GeneCards Summary for SLBP Gene

SLBP (Stem-Loop Binding Protein) is a Protein Coding gene. Diseases associated with SLBP include Wolf-Hirschhorn Syndrome. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and histone pre-mRNA DCP binding.

UniProtKB/Swiss-Prot for SLBP Gene

  • RNA-binding protein involved in the histone pre-mRNA processing. Binds the stem-loop structure of replication-dependent histone pre-mRNAs and contributes to efficient 3-end processing by stabilizing the complex between histone pre-mRNA and U7 small nuclear ribonucleoprotein (snRNP), via the histone downstream element (HDE). Plays an important role in targeting mature histone mRNA from the nucleus to the cytoplasm and to the translation machinery. Stabilizes mature histone mRNA and could be involved in cell-cycle regulation of histone gene expression. Involved in the mechanism by which growing oocytes accumulate histone proteins that support early embryogenesis. Binds to the 5 side of the stem-loop structure of histone pre-mRNAs.

Gene Wiki entry for SLBP Gene

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

Genomics for SLBP Gene

Regulatory Elements for SLBP Gene

Enhancers for SLBP 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
GH04G001757 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.8 -48.1 -48059 7.0 HDGF HDAC1 PKNOX1 FUS MLX ARID4B NFXL1 ZNF48 RAD21 GLIS2 TMEM129 FAM53A LOC100129917 NELFA CTBP1-AS2 IDUA CRIPAK SLBP FGFR3 GC04M001751
GH04G001710 1.5 FANTOM5 ENCODE 11.2 -0.7 -730 5.7 HDGF PKNOX1 ARNT CREB3L1 MLX AGO1 ZFP64 ARID4B SIN3A DMAP1 FAM53A HAUS3 NELFA CRIPAK TMEM129 SLBP ENSG00000272588 NSD2 ENSG00000270195 PIR44595
GH04G001745 1.5 Ensembl ENCODE dbSUPER 10.3 -35.4 -35368 5.1 FOXA2 MLX AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 FAM53A TMEM129 TACC3 SLBP GC04M001751 GC04P001740
GH04G001719 1.3 ENCODE dbSUPER 10.4 -9.6 -9578 5.4 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 FAM53A TMEM129 TACC3 SLBP CRIPAK ENSG00000233799 GC04P001740
GH04G001718 1.2 ENCODE dbSUPER 10.6 -5.7 -5719 1.3 HDGF ATF1 PKNOX1 AGO1 SIN3A DMAP1 ZNF48 GLIS2 KLF13 REST TMEM129 FAM53A SLBP PIR44595 ENSG00000270195
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLBP on UCSC Golden Path with GeneCards custom track

Promoters for SLBP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000164861 294 2401 HDGF PKNOX1 MLX ARNT CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1

Genomic Location for SLBP Gene

Chromosome:
4
Start:
1,692,800 bp from pter
End:
1,712,694 bp from pter
Size:
19,895 bases
Orientation:
Minus strand

Genomic View for SLBP Gene

Genes around SLBP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SLBP Gene

Proteins for SLBP Gene

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

    Protein Symbol:
    Q14493-SLBP_HUMAN
    Recommended name:
    Histone RNA hairpin-binding protein
    Protein Accession:
    Q14493
    Secondary Accessions:
    • B3KRJ5

    Protein attributes for SLBP Gene

    Size:
    270 amino acids
    Molecular mass:
    31286 Da
    Quaternary structure:
    • Monomer. SLBP/pre-mRNA complex interacts with ZNF473. Interacts with the Importin alpha/Importin beta receptor, LSM1, MIF4GD, TNPO3 and UPF1. Interaction with LSM1 occurs when histone mRNA is being rapidly degraded during the S phase. Found in a ternary complex with ERI1 and the stem-loop structure of the 3 end of histone mRNA. Associates with polyribosomes. Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Binds in a cooperative manner with ERI1 to the mature 3-end of histone mRNAs (By similarity).

    Three dimensional structures from OCA and Proteopedia for SLBP Gene

    Alternative splice isoforms for SLBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLBP Gene

Post-translational modifications for SLBP Gene

  • Phosphorylated on Thr-61 and Thr-62 in the S-phase. Phosphorylation of Thr-62 by CDK1 primes phosphorylation of Thr-61 by CK2. Phosphorylation of Thr-62 is required for its degradation by the proteasome at the end of the S phase. Its degradation is not required for histone mRNA degradation at the end of the S phase. All the phosphorylated forms detected are present in the cytoplasm. Both unphosphorylated and phosphorylated forms bind the stem-loop structure of histone mRNAs. Phosphorylation at Thr-171 increases affinity for histone mRNAs.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SLBP Gene

Domains & Families for SLBP Gene

Protein Domains for SLBP Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q14493

UniProtKB/Swiss-Prot:

SLBP_HUMAN :
  • Amino acids 31-34, 96-99 and 241-244 are necessary for interaction with the Importin alpha/Importin beta receptor. The first 18 amino acids, amino acids 69-76 and 179-182 are necessary for interaction with TNPO3. Amino acids 31-34, 96-99 and 241-244 are necessary for nuclear localization.
  • Belongs to the SLBP family.
Domain:
  • Amino acids 31-34, 96-99 and 241-244 are necessary for interaction with the Importin alpha/Importin beta receptor. The first 18 amino acids, amino acids 69-76 and 179-182 are necessary for interaction with TNPO3. Amino acids 31-34, 96-99 and 241-244 are necessary for nuclear localization.
Family:
  • Belongs to the SLBP family.
genes like me logo Genes that share domains with SLBP: view

No data available for Gene Families for SLBP Gene

Function for SLBP Gene

Molecular function for SLBP Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein involved in the histone pre-mRNA processing. Binds the stem-loop structure of replication-dependent histone pre-mRNAs and contributes to efficient 3-end processing by stabilizing the complex between histone pre-mRNA and U7 small nuclear ribonucleoprotein (snRNP), via the histone downstream element (HDE). Plays an important role in targeting mature histone mRNA from the nucleus to the cytoplasm and to the translation machinery. Stabilizes mature histone mRNA and could be involved in cell-cycle regulation of histone gene expression. Involved in the mechanism by which growing oocytes accumulate histone proteins that support early embryogenesis. Binds to the 5 side of the stem-loop structure of histone pre-mRNAs.

Gene Ontology (GO) - Molecular Function for SLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0003729 mRNA binding IDA,IEA 16912046
GO:0005515 protein binding IPI 15829567
GO:0071207 histone pre-mRNA stem-loop binding IEA,ISS --
GO:0071208 histone pre-mRNA DCP binding ISS --
genes like me logo Genes that share ontologies with SLBP: view
genes like me logo Genes that share phenotypes with SLBP: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SLBP
  • Applied Biological Materials Clones for SLBP

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLBP Gene

Localization for SLBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLBP Gene

Cytoplasm. Nucleus. Note=Polyribosome-associated. Localizes predominantly in the nucleus at the G1/G2 phases and the beginning of S phase. Through the S phase, partially redistributes to the cytoplasm. Binding to histone mRNA is necessary for cytoplasmic localization. Shuttles between the nucleus and the cytoplasm. Imported in the nucleus by the Importin alpha/Importin beta receptor.

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 SLBP gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 15829567
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 15829567
GO:0005829 cytosol TAS,IDA --
genes like me logo Genes that share ontologies with SLBP: view

Pathways & Interactions for SLBP Gene

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

Gene Ontology (GO) - Biological Process for SLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0006398 mRNA 3-end processing by stem-loop binding and cleavage ISS,IEA --
GO:0006406 mRNA export from nucleus TAS --
GO:0008334 histone mRNA metabolic process TAS --
genes like me logo Genes that share ontologies with SLBP: view

No data available for SIGNOR curated interactions for SLBP Gene

Drugs & Compounds for SLBP Gene

No Compound Related Data Available

Transcripts for SLBP Gene

Unigene Clusters for SLBP Gene

Stem-loop binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SLBP
  • Applied Biological Materials Clones for SLBP

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

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1: - -
SP2:
SP3: - - -
SP4: -

Relevant External Links for SLBP Gene

GeneLoc Exon Structure for
SLBP
ECgene alternative splicing isoforms for
SLBP

Expression for SLBP Gene

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

Protein differential expression in normal tissues from HIPED for SLBP Gene

This gene is overexpressed in Testis (42.1) and Placenta (12.6).

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



Protein tissue co-expression partners for SLBP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLBP Gene:

SLBP

SOURCE GeneReport for Unigene cluster for SLBP Gene:

Hs.298345

mRNA Expression by UniProt/SwissProt for SLBP Gene:

Q14493-SLBP_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for SLBP Gene

  • Heart(4.3)
  • Blood(4.2)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with SLBP: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLBP Gene

Orthologs for SLBP Gene

This gene was present in the common ancestor of animals.

Orthologs for SLBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLBP 34 35
  • 99.01 (n)
mouse
(Mus musculus)
Mammalia Slbp 34 16 35
  • 85.43 (n)
rat
(Rattus norvegicus)
Mammalia Slbp 34
  • 84.81 (n)
dog
(Canis familiaris)
Mammalia SLBP 34 35
  • 84.44 (n)
cow
(Bos Taurus)
Mammalia SLBP 34 35
  • 84.21 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLBP 35
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLBP 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLBP 34 35
  • 71.86 (n)
lizard
(Anolis carolinensis)
Reptilia SLBP 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slbp 34
  • 66.08 (n)
Str.8020 34
African clawed frog
(Xenopus laevis)
Amphibia SLBP 34
zebrafish
(Danio rerio)
Actinopterygii slbp 34 35
  • 60.73 (n)
Dr.26399 34
fruit fly
(Drosophila melanogaster)
Insecta Slbp 35
  • 21 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea cdl-1 35
  • 17 (a)
OneToOne
Species where no ortholog for SLBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for SLBP Gene

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

Paralogs for SLBP Gene

Pseudogenes.org Pseudogenes for SLBP Gene

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

No data available for Paralogs for SLBP Gene

Variants for SLBP Gene

Sequence variations from dbSNP and Humsavar for SLBP Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000154192 -- 1,695,038(+) CGGAT(A/G)GCAAT intron-variant
rs1000268056 -- 1,700,429(+) TTCCT(A/G)AGGCA intron-variant
rs1000379677 -- 1,707,680(+) ACAGG(A/C)TCATG intron-variant
rs1000648124 -- 1,714,526(+) GACAG(A/G)GTAAG upstream-variant-2KB
rs1000662263 -- 1,712,202(+) GGGCC(A/C/G)GGCGC utr-variant-5-prime

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

Variant ID Type Subtype PubMed ID
dgv5081n100 CNV gain 25217958
dgv8901n54 CNV loss 21841781
esv2759218 CNV gain 17122850
esv3599394 CNV loss 21293372
nsv1114479 CNV deletion 24896259
nsv1161027 CNV deletion 26073780
nsv428434 CNV gain 18775914
nsv470000 CNV loss 18288195
nsv508989 CNV insertion 20534489
nsv593316 CNV gain 21841781
nsv949756 CNV deletion 24416366

Variation tolerance for SLBP Gene

Residual Variation Intolerance Score: 32.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLBP Gene

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

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

Disorders for SLBP Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLBP Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • 4p deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SLBP in MalaCards View complete list of genes associated with diseases

Relevant External Links for SLBP

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLBP
genes like me logo Genes that share disorders with SLBP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLBP Gene

Publications for SLBP Gene

  1. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. (PMID: 9049306) Martin F. … Mueller B. (EMBO J. 1997) 2 3 4 22 64
  2. Knockdown of SLBP results in nuclear retention of histone mRNA. (PMID: 19155325) Sullivan K.D. … Wagner E.J. (RNA 2009) 3 4 22 64
  3. SLIP1, a factor required for activation of histone mRNA translation by the stem-loop binding protein. (PMID: 18025107) Cakmakci N.G. … Marzluff W.F. (Mol. Cell. Biol. 2008) 3 4 22 64
  4. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. (PMID: 18172165) Mullen T.E. … Marzluff W.F. (Genes Dev. 2008) 3 4 22 64
  5. Phosphorylation of threonine 61 by cyclin a/Cdk1 triggers degradation of stem-loop binding protein at the end of S phase. (PMID: 18490441) Koseoglu M.M. … Marzluff W.F. (Mol. Cell. Biol. 2008) 3 4 22 64

Products for SLBP Gene

  • Addgene plasmids for SLBP

Sources for SLBP Gene

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