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SLBP stem-loop binding protein [ Homo sapiens (human) ]

Gene ID: 7884, updated on 9-Jan-2019

Summary

Official Symbol
SLBPprovided by HGNC
Official Full Name
stem-loop binding proteinprovided by HGNC
Primary source
HGNC:HGNC:10904
See related
Ensembl:ENSG00000163950 MIM:602422
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HBP
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 30.6), bone marrow (RPKM 27.2) and 25 other tissues See more
Orthologs

Genomic context

See SLBP in Genome Data Viewer
Location:
4p16.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (1692731..1715876, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1694527..1714421, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 53 member A Neighboring gene VISTA enhancer hs526 Neighboring gene uncharacterized LOC105374349 Neighboring gene transmembrane protein 129 Neighboring gene transforming acidic coiled-coil containing protein 3 Neighboring gene uncharacterized LOC112268460

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
histone pre-mRNA DCP binding ISS
Inferred from Sequence or Structural Similarity
more info
 
histone pre-mRNA stem-loop binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone pre-mRNA stem-loop binding ISS
Inferred from Sequence or Structural Similarity
more info
 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone mRNA metabolic process TAS
Traceable Author Statement
more info
 
mRNA 3'-end processing by stem-loop binding and cleavage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-end processing by stem-loop binding and cleavage ISS
Inferred from Sequence or Structural Similarity
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA transport IDA
Inferred from Direct Assay
more info
PubMed 
nuclear DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
histone pre-mRNA 3'end processing complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone pre-mRNA 3'end processing complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
histone RNA hairpin-binding protein
Names
hairpin binding protein, histone
histone binding protein
histone stem-loop binding protein
stem-loop (histone) binding protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001306074.1NP_001293003.1  histone RNA hairpin-binding protein isoform 2

    See identical proteins and their annotated locations for NP_001293003.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AK094257, AK300826, BM976632, DA064026, DB027411, DB031118, DC383752, Z71188
    Consensus CDS
    CCDS77889.1
    UniProtKB/Swiss-Prot
    Q14493
    UniProtKB/TrEMBL
    B3KST9, B4DUW7, E7EUV9
    Related
    ENSP00000418658.1, ENST00000488267.5
    Conserved Domains (1) summary
    pfam15247
    Location:95162
    SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
  2. NM_001306075.1NP_001293004.1  histone RNA hairpin-binding protein isoform 3

    See identical proteins and their annotated locations for NP_001293004.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    AK091735, AK094257, BM976632, DA064026, DC383752
    Consensus CDS
    CCDS82903.1
    UniProtKB/Swiss-Prot
    Q14493
    UniProtKB/TrEMBL
    B3KST9
    Related
    ENSP00000406322.2, ENST00000429429.6
    Conserved Domains (1) summary
    pfam15247
    Location:91158
    SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
  3. NM_006527.4NP_006518.1  histone RNA hairpin-binding protein isoform 1

    See identical proteins and their annotated locations for NP_006518.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK093314, AK094257, BM976632, U75679
    Consensus CDS
    CCDS3350.1
    UniProtKB/Swiss-Prot
    Q14493
    UniProtKB/TrEMBL
    B3KSC5, B3KST9, Q53XR2
    Related
    ENSP00000417686.1, ENST00000489418.5
    Conserved Domains (2) summary
    pfam15247
    Location:130197
    SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
    pfam16214
    Location:587
    AC_N; Adenylyl cyclase N-terminal extracellular and transmembrane region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    1692731..1715876 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_002959759.1 RNA Sequence

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