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. Expressi... See more...

Aliases for SLBP Gene

Aliases for SLBP Gene

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

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 and Epiphyseal Dysplasia, Multiple, 3. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Tat-mediated elongation of the HIV-1 transcript. Gene Ontology (GO) annotations related to this gene include histone pre-mRNA DCP binding.

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

Genomics for SLBP Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLBP 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
GH04J001710 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 261.1 +2.6 2644 6.1 BCLAF1 SP1 ZNF207 ZNF600 MYC IKZF1 SIX5 JUND ZNF580 ZNF592 SLBP-DT SLBP HSALNG0032308 TACC3 RNF4 FAM53A FAM193A NELFA HAUS3 UVSSA
GH04J001717 Enhancer 0.6 ENCODE dbSUPER 250.7 -1.7 -1712 0.3 HNRNPL POLR2A RBFOX2 HIC1 HSALNG0032310 SLBP FAM53A TMEM129 TACC3
GH04J001719 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.5 -6.2 -6203 5.8 BCLAF1 SP1 ZNF207 MYC ZNF600 SIX5 ZNF592 POLR2A ZIC2 ZBTB10 TMEM129 TACC3 HSALNG0032311 piR-50596 FAM53A SLBP ENSG00000233799 piR-57460-497 FGFR3
GH04J001682 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.2 +31.5 31450 3.1 ZNF207 MYC JUND ZNF592 NFIC NONO BHLHE40 TBP SIN3B RUNX1 FAM53A ENSG00000207009 lnc-TACC3-3 piR-60429 SLBP TMEM129 HSALNG0032304 TACC3
GH04J001725 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 10.5 -11.3 -11265 3.8 BCLAF1 ZNF654 JUND CTCF REST TRIM22 SIN3A SAP130 RAD21 SMC3 piR-32214-499 FAM53A TMEM129 SLBP TACC3 HSALNG0032313 FGFR3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLBP on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLBP

Top Transcription factor binding sites by QIAGEN in the SLBP gene promoter:
  • AML1a
  • HTF
  • NF-E2
  • NF-E2 p45
  • Nkx2-5
  • p53

Genomic Locations for SLBP Gene

Latest Assembly
chr4:1,692,731-1,715,876
(GRCh38/hg38)
Size:
23,146 bases
Orientation:
Minus strand

Previous Assembly
chr4:1,694,458-1,714,046
(GRCh37/hg19 by Entrez Gene)
Size:
19,589 bases
Orientation:
Minus strand

chr4:1,694,527-1,714,282
(GRCh37/hg19 by Ensembl)
Size:
19,756 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

Antibodies for research

  • Abcam antibodies for SLBP
  • Boster Bio Antibodies for SLBP

No data available for DME Specific Peptides for SLBP Gene

Domains & Families for SLBP Gene

Gene Families for SLBP Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SLBP Gene

Suggested Antigen Peptide Sequences for SLBP Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ34416 fis, clone HEART2006310, highly similar to Histone RNA hairpin-binding protein (B3KRJ5_HUMAN)
  • cDNA FLJ35995 fis, clone TESTI2014979, highly similar to Histone RNA hairpin-binding protein (B3KSC5_HUMAN)
  • cDNA, FLJ96722, Homo sapiens stem-loop (histone) binding protein (SLBP), mRNA (Q53XR2_HUMAN)
  • Histone stem-loop-binding protein (SLBP_HUMAN)

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

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.

Phenotypes From GWAS Catalog for SLBP Gene

Gene Ontology (GO) - Molecular Function for SLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,HDA 22658674
GO:0003729 mRNA binding IEA,IDA 16912046
GO:0005515 protein binding IPI 15829567
GO:0042802 identical protein binding IPI 23286197
GO:0071207 histone pre-mRNA stem-loop binding IEA,ISS --
genes like me logo Genes that share ontologies with SLBP: view
genes like me logo Genes that share phenotypes with SLBP: view

Animal Models for SLBP Gene

MGI Knock Outs for SLBP:
  • Slbp Slbp<tm1.1(KOMP)Vlcg>

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 15829567
GO:0005654 nucleoplasm IDA,TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 15829567
GO:0005829 cytosol IDA,TAS --
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 IEA,ISS --
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

mRNA/cDNA for SLBP Gene

3 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

Expression for SLBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for SLBP Gene



Protein tissue co-expression partners for SLBP Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

  • Blood(4.4)
  • Heart(4.4)
  • Nervous system(3.1)
  • Skin(2.5)
  • Kidney(2.3)
  • Lung(2.3)
  • Liver(2.2)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with SLBP: view

Primer products for research

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 29 30
  • 99.01 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Slbp 29 16 30
  • 85.43 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Slbp 29
  • 84.81 (n)
Dog
(Canis familiaris)
Mammalia SLBP 29 30
  • 84.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SLBP 29 30
  • 84.21 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SLBP 30
  • 81 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SLBP 30
  • 79 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SLBP 29 30
  • 71.86 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SLBP 30
  • 69 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slbp 29
  • 66.08 (n)
Str.8020 29
African clawed frog
(Xenopus laevis)
Amphibia SLBP 29
Zebrafish
(Danio rerio)
Actinopterygii slbp 29 30
  • 60.73 (n)
OneToOne
Dr.26399 29
Fruit Fly
(Drosophila melanogaster)
Insecta Slbp 30
  • 21 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea cdl-1 30
  • 17 (a)
OneToOne
Species where no ortholog for SLBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for SLBP: view image
Alliance of Genome Resources:
Additional Orthologs for SLBP

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

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SLBP Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for SLBP Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLBP Gene

Disorders for SLBP Gene

MalaCards: The human disease database

(4) MalaCards diseases for SLBP Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search SLBP in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 … Müller B (The EMBO journal 1997) 2 3 4 22
  2. Knockdown of SLBP results in nuclear retention of histone mRNA. (PMID: 19155325) Sullivan KD … Wagner EJ (RNA (New York, N.Y.) 2009) 3 4 22
  3. Phosphorylation of threonine 61 by cyclin a/Cdk1 triggers degradation of stem-loop binding protein at the end of S phase. (PMID: 18490441) Koseoglu MM … Marzluff WF (Molecular and cellular biology 2008) 3 4 22
  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 TE … Marzluff WF (Genes & development 2008) 3 4 22
  5. SLIP1, a factor required for activation of histone mRNA translation by the stem-loop binding protein. (PMID: 18025107) Cakmakci NG … Marzluff WF (Molecular and cellular biology 2008) 3 4 22

Products for SLBP Gene

Sources for SLBP Gene