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Gene: RNU5B-1 (RNA, U5B small nuclear 1) Homo sapiens

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Symbol:

RNU5B-1

Name:

RNA, U5B small nuclear 1

RGD ID:

1345743

HGNC Page

HGNC:10212

Description:

Predicted to be involved in formation of quadruple SL/U4/U5/U6 snRNP and spliceosomal tri-snRNP complex assembly. Predicted to be part of U4/U6 x U5 tri-snRNP complex and U5 snRNP.

Type:

snrna

RefSeq Status:

VALIDATED

Previously known as:

RNU5B; RNU5B-1P; U5B1

RGD Orthologs

Mouse

Rat

Dog

Alliance Orthologs

More Info

more info ...

Related Pseudogenes:

RNU5B-2P RNU5B-3P RNU5B-4P RNU5B-5P RNU5B-6P

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	65,304,677 - 65,304,793 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	15	65,304,677 - 65,304,792 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	15	65,597,015 - 65,597,131 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	63,384,068 - 63,384,184 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	76,613,646 - 76,613,679	NCBI
Celera	15	42,475,189 - 42,475,305 (+)	NCBI		Celera
Cytogenetic Map	15	q22.31	NCBI
HuRef	15	42,421,022 - 42,421,138 (+)	NCBI		HuRef
CHM1_1	15	65,716,738 - 65,716,854 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	15	63,114,055 - 63,114,171 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Neurodevelopmental Disorders (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2-hydroxypropanoic acid (EXP)

doxorubicin (EXP)

potassium chromate (EXP)

rac-lactic acid (EXP)

thiram (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

formation of quadruple SL/U4/U5/U6 snRNP (IEA)

spliceosomal tri-snRNP complex assembly (IEA)

Cellular Component

U4/U6 x U5 tri-snRNP complex (IEA)

U5 snRNP (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Three novel functional variants of human U5 small nuclear RNA.	Sontheimer EJ and Steitz JA, Mol Cell Biol 1992 Feb;12(2):734-46.

Additional References at PubMed

PMID:6164980	PMID:22751105	PMID:37059803

Genomics

Comparative Map Data

RNU5B-1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	65,304,677 - 65,304,793 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	15	65,304,677 - 65,304,792 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	15	65,597,015 - 65,597,131 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	63,384,068 - 63,384,184 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	76,613,646 - 76,613,679	NCBI
Celera	15	42,475,189 - 42,475,305 (+)	NCBI		Celera
Cytogenetic Map	15	q22.31	NCBI
HuRef	15	42,421,022 - 42,421,138 (+)	NCBI		HuRef
CHM1_1	15	65,716,738 - 65,716,854 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	15	63,114,055 - 63,114,171 (+)	NCBI		T2T-CHM13v2.0

Gm25313
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	65,103,854 - 65,103,969 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	65,103,854 - 65,103,969 (-)	Ensembl		GRCm39 Ensembl
GRCm38	9	65,196,572 - 65,196,687 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	65,196,572 - 65,196,687 (-)	Ensembl	GRCm38		mm10	GRCm38
Cytogenetic Map	9	C	NCBI

LOC120094550
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	74,612,687 - 74,612,802 (-)	NCBI		GRCr8
mRatBN7.2	8	65,717,512 - 65,717,627 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	65,717,512 - 65,717,627 (-)	Ensembl		mRatBN7.2 Ensembl
Cytogenetic Map	8	q24	NCBI

LOC119866956
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Dog10K_Boxer_Tasha	30	29,597,404 - 29,597,519 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	30	29,858,660 - 29,858,775 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	30	29,858,660 - 29,858,775 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	30	29,789,474 - 29,789,589 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	30	29,851,215 - 29,851,330 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	30	30,093,389 - 30,093,504 (+)	NCBI		UU_Cfam_GSD_1.0

Variants

Variants in RNU5B-1
4 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3	copy number gain	See cases [RCV000142915]	Chr15:59828460..101920998 [GRCh38] Chr15:60120659..102461201 [GRCh37] Chr15:57907951..100278724 [NCBI36] Chr15:15q22.2-26.3	pathogenic
GRCh38/hg38 15q22.31(chr15:64448836-65975439)x3	copy number gain	See cases [RCV000052344]	Chr15:64448836..65975439 [GRCh38] Chr15:64741035..66267777 [GRCh37] Chr15:62528088..64054831 [NCBI36] Chr15:15q22.31	pathogenic
NR_002757.3(RNU5B-1):n.24G>C	single nucleotide variant	RNU5B-1-associated neurodevelopmental disorder [RCV004764400]	Chr15:65304700 [GRCh38] Chr15:65597038 [GRCh37] Chr15:15q22.31	uncertain significance
NR_002757.3(RNU5B-1):n.39C>G	single nucleotide variant	RNU5B-1-associated neurodevelopmental disorder [RCV004764401]	Chr15:65304715 [GRCh38] Chr15:65597053 [GRCh37] Chr15:15q22.31	likely pathogenic
NR_002757.3(RNU5B-1):n.44A>G	single nucleotide variant	Neurodevelopmental disorder [RCV004797650]\|RNU5B-1-associated neurodevelopmental disorder [RCV004764402]	Chr15:65304720 [GRCh38] Chr15:65597058 [GRCh37] Chr15:15q22.31	likely pathogenic\|uncertain significance
NR_002757.3(RNU5B-1):n.74T>C	single nucleotide variant	RNU5B-1-associated neurodevelopmental disorder [RCV004764403]	Chr15:65304750 [GRCh38] Chr15:65597088 [GRCh37] Chr15:15q22.31	uncertain significance

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	38
Count of miRNA genes:	38
Interacting mature miRNAs:	38
Transcripts:	ENST00000363286
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

adipose tissue	alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	entire extraembryonic component	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system
543	518	757	410	1505	415	594	3	104	525	74	811	1655	1645	41	1208	181	677	462	38

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_002757	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC105129	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068263	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X04293	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000363286

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	65,304,677 - 65,304,792 (+)	Ensembl

RefSeq Acc Id:

NR_002757

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	15	65,304,677 - 65,304,793 (+)	NCBI
GRCh37	15	65,597,015 - 65,597,131 (+)	RGD
Build 36	15	63,384,068 - 63,384,184 (+)	NCBI Archive
Celera	15	42,475,189 - 42,475,305 (+)	RGD
HuRef	15	42,421,022 - 42,421,138 (+)	ENTREZGENE
CHM1_1	15	65,716,738 - 65,716,854 (+)	NCBI
T2T-CHM13v2.0	15	63,114,055 - 63,114,171 (+)	NCBI

Sequence:

show sequence

ATACTCTGGTTTCTCTTCAGATCGTATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAG
GAACAACTCTGAGTCTTAAGCTAATTTTTTGAGGCCTTGTTCCGACAAGGCTA

hide sequence

Promoters

RGD ID:

6792289

Promoter ID:

HG_KWN:21678

Type:

Non-CpG

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, CD4+TCell_2Hour, HeLa_S3, Jurkat, K562, Lymphoblastoid, NB4

Transcripts:

ENST00000363286

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	15	63,384,066 - 63,384,566 (+)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	RNU5B-1	COSMIC
Ensembl Genes	ENSG00000200156	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000363286	ENTREZGENE
GTEx	ENSG00000200156	GTEx
HGNC ID	HGNC:10212	ENTREZGENE
Human Proteome Map	RNU5B-1	Human Proteome Map
NCBI Gene	26832	ENTREZGENE
PharmGKB	PA34579	PharmGKB
RNAcentral	URS00006E1BD2	RNACentral
	URS000075B029	RNACentral

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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