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

    Gene ID: 4809, updated on 14-Nov-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
    mouse all
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    Genomic context

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    See SNU13 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41673933..41690480, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42152913..42169470, complement)
    RS_2024_09 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 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. Cloning and mapping of a human novel cDNA (NHP2L1) that encodes a protein highly homologous to yeast nuclear protein NHP2. Saito H, et al. Cytogenet Cell Genet, 1996. PMID 8978773
    2. 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
    3. Molecular cloning and sequencing of cDNA encoding for human FA-1 antigen. Naz RK, et al. Mol Reprod Dev, 2002 Oct. PMID 12203836
    4. 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
    5. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Vidovic I, et al. Mol Cell, 2000 Dec. PMID 11163207

    See all (152) 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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    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)

    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 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 
    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_2024_08

    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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