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

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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 4p16.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (1692731..1712319, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (1690606..1710149, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (1694458..1714046, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DRAIC promotes growth of breast cancer by sponging miR-432-5p to upregulate SLBP.
Title: DRAIC promotes growth of breast cancer by sponging miR-432-5p to upregulate SLBP.
Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription.
Title: Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription.
Knocking down miR-384 promotes growth and metastasis of osteosarcoma MG63 cells by targeting SLBP
Title: Knocking down miR-384 promotes growth and metastasis of osteosarcoma MG63 cells by targeting SLBP.
SLBP is a potentially important cellular regulator of HIV-1, thereby establishing a link between histone metabolism, inflammation, and HIV-1 infection
Title: Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication.
showed that inhibiting the SLBP mRNA and protein levels were rescued by epigenetic modifiers suggesting that nickel's effects on SLBP may be mediated via epigenetic mechanisms
Title: Nickel and cadmium-induced SLBP depletion: A potential pathway to metal mediated cellular transformation.
Cyclin F-mediated degradation of SLBP limits H2A.X accumulation and apoptosis upon genotoxic stress in G2 cell cycle checkpoint.
Title: Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2.
CRL4(WDR23) is required for efficient histone mRNA 3' end processing to produce mature histone mRNAs for translation. CRL4(WDR23) binds and ubiquitylates SLBP in vitro and in vivo, and this modification activates SLBP function in histone mRNA 3' end processing without affecting its protein levels.
Title: CRL4(WDR23)-Mediated SLBP Ubiquitylation Ensures Histone Supply during DNA Replication.
FEM1 proteins are ancient regulators of Stem-Loop Binding Protein.
Title: FEM1 proteins are ancient regulators of SLBP degradation.
CRL4-DCAF11 mediates the degradation of SLBP at the end of S phase and this degradation is essential for the viability of cells.
Title: DDB1 and CUL4 associated factor 11 (DCAF11) mediates degradation of Stem-loop binding protein at the end of S phase.
arsenic, a carcinogenic metal, decreases cellular levels of SLBP by inducing its proteasomal degradation and inhibiting SLBP transcription via epigenetic mechanisms
Title: Arsenic induces polyadenylation of canonical histone mRNA by down-regulating stem-loop-binding protein gene expression.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH27233 (e-PCR)
- UniSTS:85574

SHGC-67765 (e-PCR)
- UniSTS:67453

WI-11359 (e-PCR)
- UniSTS:67276

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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

Go to the top of the page Help

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)

Go to the top of the page Help

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)

NM_001306074.2 → NP_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:95 → 163

SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
NM_001306075.2 → NP_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:91 → 158

SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain
NM_006527.4 → NP_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:130 → 198

SLBP_RNA_bind; Histone RNA hairpin-binding protein RNA-binding domain