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

Summary

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

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_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.

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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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

IB1149 (e-PCR)
- UniSTS:6198

RH15753 (e-PCR)
- UniSTS:91710

RH47477 (e-PCR)
- UniSTS:19613

SHGC-7075 (e-PCR)
- UniSTS:44781

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA binding	HDA more info	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

NG_051551.1 RefSeqGene

Range

6626..21560

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1102

mRNA and Protein(s)

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
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