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

    Gene ID: 7884, updated on 9-Dec-2024

    Summary

    Official Symbol
    SLBPprovided by HGNC
    Official Full Name
    stem-loop histone mRNA binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:10904
    See related
    Ensembl:ENSG00000163950 MIM:602422; AllianceGenome:HGNC:10904
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLBP in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1692731..1712319, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1690606..1710149, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1694458..1714046, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1513782-1514432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1522059-1522612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1545561-1546304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1546305-1547046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1550615-1551471 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1553567-1553737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1562577-1563106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568111-1568928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568929-1569747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1569748-1570565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1573296-1574073 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1574074-1574850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1577987-1578860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1578861-1579734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1579735-1580607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15134 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1582889-1583115 Neighboring gene family with sequence similarity 53 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1595837-1596352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1600440-1601266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1605640-1606631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1606632-1607622 Neighboring gene VISTA enhancer hs526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1616583-1617084 Neighboring gene uncharacterized LOC105374349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1648945-1649446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15137 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1686561-1687180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1687181-1687800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1707982-1708482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1723083-1724078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1732480-1732980 Neighboring gene transmembrane protein 129, E3 ubiquitin ligase Neighboring gene uncharacterized LOC112268460 Neighboring gene transforming acidic coiled-coil containing protein 3

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables histone pre-mRNA DCP binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone pre-mRNA stem-loop binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone pre-mRNA stem-loop binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cap-dependent translational initiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA 3'-end processing by stem-loop binding and cleavage IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA 3'-end processing by stem-loop binding and cleavage ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mRNA transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of histone mRNA stem-loop binding complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of histone pre-mRNA 3'end processing complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of histone pre-mRNA 3'end processing complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of 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
    stem-loop binding protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001306074.2NP_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, DB027411, DB031118, Z71188
      Consensus CDS
      CCDS77889.1
      UniProtKB/TrEMBL
      B4DUW7, E7EUV9
      Related
      ENSP00000418658.1, ENST00000488267.5
      Conserved Domains (1) summary
      pfam15247
      Location:95163
      SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
    2. NM_001306075.2NP_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
      Consensus CDS
      CCDS82903.1
      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
      B3KRJ5, Q14493
      UniProtKB/TrEMBL
      B3KST9, D3DVP7, Q53XR2
      Related
      ENSP00000417686.1, ENST00000489418.6
      Conserved Domains (1) summary
      pfam15247
      Location:130198
      SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      1692731..1712319 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      1690606..1710149 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350815.1XP_054206790.1  histone RNA hairpin-binding protein isoform X1

      UniProtKB/TrEMBL
      B3KSC5