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SNU13 small nuclear ribonucleoprotein 13 [ Homo sapiens (human) ]

Gene ID: 4809, updated on 11-Apr-2024

Summary

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Official Symbol
SNU13provided by HGNC
Official Full Name
small nuclear ribonucleoprotein 13provided by HGNC
Primary source
HGNC:HGNC:7819
See related
Ensembl:ENSG00000100138 MIM:601304; AllianceGenome:HGNC:7819
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
FA1; FA-1; NHPX; 15.5K; OTK27; SSFA1; NHP2L1; SPAG12; SNRNP15-5
Summary
Originally named because of its sequence similarity to the Saccharomyces cerevisiae NHP2 (non-histone protein 2), this protein appears to be a highly conserved nuclear protein that is a component of the [U4/U6.U5] tri-snRNP. It binds to the 5' stem-loop of U4 snRNA. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 32.6), adrenal (RPKM 31.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q13.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41673933..41690480, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42152913..42169470, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42069937..42084871, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene desumoylating isopeptidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19124 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42016465-42017066 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42026409-42027062 Neighboring gene X-ray repair cross complementing 6 Neighboring gene protein LLP homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19125 Neighboring gene RNA, U6 small nuclear 476, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr22:42084352-42084551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19128 Neighboring gene CTA-216E10.6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13796 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene10 Neighboring gene meiotic double-stranded break formation protein 1 Neighboring gene RNA, U6atac small nuclear 22, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Functional implications for a prototypical K-turn binding protein from structural and dynamical studies of 15.5K. Soss SE, et al. Biochemistry, 2007 Dec 25. PMID 18044964
  2. Molecular cloning and sequencing of cDNA encoding for human FA-1 antigen. Naz RK, et al. Mol Reprod Dev, 2002 Oct. PMID 12203836
  3. In vivo analysis of NHPX reveals a novel nucleolar localization pathway involving a transient accumulation in splicing speckles. Leung AK, et al. J Cell Biol, 2002 May 13. PMID 12011111, Free PMC Article
  4. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Vidovic I, et al. Mol Cell, 2000 Dec. PMID 11163207
  5. Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA. Nottrott S, et al. EMBO J, 1999 Nov 1. PMID 10545122, Free PMC Article

See all (134) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results solve the structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Also, it seems that the complexes involving NUFIP1, ZNHIT3, and SNU13 share strong structural similarities between human and yeast, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species.
    Title: Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species.
  2. snoRNP assembly factor NUFIP can regulate the interactions between TIP48 and TIP49 and the core box C/D proteins.
    Title: Evidence that the AAA+ proteins TIP48 and TIP49 bridge interactions between 15.5K and the related NOP56 and NOP58 proteins during box C/D snoRNP biogenesis.
  3. the testis-specific expression of FA-1 antigen at the mRNA level
    Title: Molecular cloning and sequencing of cDNA encoding for human FA-1 antigen.
  4. describe the solution NMR structure of free 15.5K, as well as studies of conformational flexibility from 15N NMR relaxation and H/D exchange experiments
    Title: Functional implications for a prototypical K-turn binding protein from structural and dynamical studies of 15.5K.
  5. NHPX is specifically accumulated in both nucleoli and Cajal bodies (CBs) in vivo. The data show a specific temporal pathway involving the sequential and directed accumulation of NHPX in distinct subnuclear compartments
    Title: In vivo analysis of NHPX reveals a novel nucleolar localization pathway involving a transient accumulation in splicing speckles.
  6. Data show that binding of the 15.5 kD RNA binding protein to the box C/D motif of snoRNAs is essential for the association of other snoRNP-associated proteins.
    Title: Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP.
Submit: New GeneRIF Correction

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Expression of HIV-1 Tat upregulates the abundance of NHP2 non-histone chromosome protein 2-like 1 (NHP2L1) in the nucleoli of Jurkat T-cells PubMed
nucleocapsid gag HIV-1 NC is identified to have a physical interaction with NHP2 non-histone chromosome protein 2-like 1 (NHP2L1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables U3 snoRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables U4 snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables U4atac snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables box C/D sno(s)RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to snoRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in box C/D snoRNP assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in maturation of SSU-rRNA IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosomal small subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in single fertilization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of U4atac snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of box C/D methylation guide snoRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of box C/D methylation guide snoRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of box C/D methylation guide snoRNP complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in dense fibrillar component IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of small-subunit processome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
NHP2-like protein 1
Names
NHP2 non-histone chromosome protein 2-like 1
SNU13 homolog, small nuclear ribonucleoprotein (U4/U6.U5)
U4/U6.U5 tri-snRNP 15.5 kDa protein
[U4/U6.U5] tri-snRNP 15.5 kD RNA binding protein
high mobility group-like nuclear protein 2 homolog 1
non-histone chromosome protein 2-like 1
sperm specific antigen 1

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_051551.1 RefSeqGene

    Range
    6626..21560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1102

mRNA and Protein(s)

  1. NM_001003796.2 → NP_001003796.1  NHP2-like protein 1

    See identical proteins and their annotated locations for NP_001003796.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 use different start codons but encode the same protein.
    Source sequence(s)
    BI770951, CF552526, D50420
    Consensus CDS
    CCDS33653.1
    UniProtKB/Swiss-Prot
    P55769
    UniProtKB/TrEMBL
    Q6FHM6
    Related
    ENSP00000383949.1, ENST00000401959.6
    Conserved Domains (1) summary
    cd21104
    Location:7 → 128
    SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13

  2. NM_005008.4 → NP_004999.1  NHP2-like protein 1

    See identical proteins and their annotated locations for NP_004999.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC019282, D50420, DB021462
    Consensus CDS
    CCDS14022.1
    UniProtKB/Swiss-Prot
    P55769
    UniProtKB/TrEMBL
    Q6FHM6
    Related
    ENSP00000497142.1, ENST00000648674.1
    Conserved Domains (1) summary
    cd21104
    Location:7 → 128
    SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    41673933..41690480 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028811.2 → XP_016884300.1  NHP2-like protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    42152913..42169470 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325659.1 → XP_054181634.1  NHP2-like protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55769.3 GenPept UniProtKB/Swiss-Prot:P55769

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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