RNU5F-1 (RNA, U5F small nuclear 1) - Rat Genome Database

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Gene: RNU5F-1 (RNA, U5F small nuclear 1) Homo sapiens
Analyze
Symbol: RNU5F-1
Name: RNA, U5F small nuclear 1
RGD ID: 1344416
HGNC Page HGNC:10216
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; INTERACTS WITH 2-hydroxypropanoic acid; aflatoxin B1; Aflatoxin B2 alpha.
Type: snrna
RefSeq Status: VALIDATED
Previously known as: RNU5F; U5F
RGD Orthologs
Mouse
Rat
Dog
Alliance Genes
More Info more info ...
Related Pseudogenes: RNU5F-6P   RNU5F-8P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Note: RNU5F (GeneID 26828) was annotated incorrectly on NCBI's Build 37.2. Its correct location is chr1:45187458..45187573(-). [17 Jun 2014]
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38144,721,786 - 44,721,901 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl144,721,786 - 44,721,902 (-)EnsemblGRCh38hg38GRCh38
GRCh37145,187,458 - 45,187,573 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,960,045 - 44,960,160 (-)NCBINCBI36Build 36hg18NCBI36
Celera2214,106,517 - 14,106,577 (-)NCBICelera
Cytogenetic Map1p34.1NCBI
HuRef143,300,991 - 43,301,106 (-)NCBIHuRef
CHM1_1145,303,368 - 45,303,483 (-)NCBICHM1_1
T2T-CHM13v2.0144,592,727 - 44,592,842 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. 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:29117863  


Genomics

Comparative Map Data
RNU5F-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38144,721,786 - 44,721,901 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl144,721,786 - 44,721,902 (-)EnsemblGRCh38hg38GRCh38
GRCh37145,187,458 - 45,187,573 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,960,045 - 44,960,160 (-)NCBINCBI36Build 36hg18NCBI36
Celera2214,106,517 - 14,106,577 (-)NCBICelera
Cytogenetic Map1p34.1NCBI
HuRef143,300,991 - 43,301,106 (-)NCBIHuRef
CHM1_1145,303,368 - 45,303,483 (-)NCBICHM1_1
T2T-CHM13v2.0144,592,727 - 44,592,842 (-)NCBIT2T-CHM13v2.0
Gm23143
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394117,059,725 - 117,059,840 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4117,059,725 - 117,059,840 (+)EnsemblGRCm39 Ensembl
GRCm384117,202,528 - 117,202,643 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4117,202,528 - 117,202,643 (+)EnsemblGRCm38mm10GRCm38
Cytogenetic Map4D1NCBI
LOC120103376
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85135,903,593 - 135,903,708 (+)NCBIGRCr8
mRatBN7.25130,667,018 - 130,667,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5130,667,018 - 130,667,133 (+)EnsemblmRatBN7.2 Ensembl
Cytogenetic Map5q36NCBI
LOC119870595
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha280,895,043 - 80,895,159 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0285,023,447 - 85,023,563 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl285,023,447 - 85,023,563 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1281,772,637 - 81,772,753 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0282,772,833 - 82,772,949 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0283,838,226 - 83,838,342 (-)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_004446.2(EPRS):c.2746C>T (p.Arg916Trp) single nucleotide variant Malignant melanoma [RCV000064539] Chr1:219988619 [GRCh38]
Chr1:220161961 [GRCh37]
Chr1:218228584 [NCBI36]
Chr1:1q41		 not provided
NM_018060.3(IARS2):c.1108C>T (p.Pro370Ser) single nucleotide variant Malignant melanoma [RCV000064540] Chr1:220105932 [GRCh38]
Chr1:220279274 [GRCh37]
Chr1:218345897 [NCBI36]
Chr1:1q41		 not provided
GRCh38/hg38 1p34.1(chr1:43896056-44867736)x3 copy number gain See cases [RCV000142581] Chr1:43896056..44867736 [GRCh38]
Chr1:44361728..45333408 [GRCh37]
Chr1:44134315..45105995 [NCBI36]
Chr1:1p34.1		 uncertain significance
GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3 copy number gain See cases [RCV000051803] Chr1:38222737..45636176 [GRCh38]
Chr1:38688409..46101848 [GRCh37]
Chr1:38460996..45874435 [NCBI36]
Chr1:1p34.3-34.1		 pathogenic
GRCh38/hg38 1p34.3-33(chr1:39479787-47688131)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|See cases [RCV000051817] Chr1:39479787..47688131 [GRCh38]
Chr1:39945459..48153803 [GRCh37]
Chr1:39718046..47926390 [NCBI36]
Chr1:1p34.3-33		 pathogenic
GRCh38/hg38 1p34.1(chr1:44713837-45282899)x3 copy number gain See cases [RCV000051129] Chr1:44713837..45282899 [GRCh38]
Chr1:45179509..45748571 [GRCh37]
Chr1:44952096..45521158 [NCBI36]
Chr1:1p34.1		 uncertain significance
Single allele inversion Bilateral polymicrogyria [RCV003459046] Chr1:33246132..61045156 [GRCh38]
Chr1:1p35.1-31.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:186
Interacting mature miRNAs:194
Transcripts:ENST00000362507
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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 13 15 12 91 1 2 6 19 2 20 13 4 1 3
Low 452 238 603 242 558 214 1077 143 1285 122 683 522 32 389 540 2 2
Below cutoff 484 370 370 125 225 89 710 238 1016 55 213 264 37 281 405

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000362507
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl144,721,786 - 44,721,902 (-)Ensembl
RefSeq Acc Id: NR_002753
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38144,721,786 - 44,721,901 (-)NCBI
GRCh37145,187,458 - 45,187,573 (-)ENTREZGENE
Build 36144,960,045 - 44,960,160 (-)NCBI Archive
Celera114,106,517 - 14,106,577 (-)RGD
HuRef143,300,991 - 43,301,106 (-)ENTREZGENE
CHM1_1145,303,368 - 45,303,483 (-)NCBI
T2T-CHM13v2.0144,592,727 - 44,592,842 (-)NCBI
Sequence:
Promoters
RGD ID:6785411
Promoter ID:HG_KWN:2443
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:ENST00000362507
Position:
Human AssemblyChrPosition (strand)Source
Build 36144,959,719 - 44,960,219 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC RNU5F-1 COSMIC
Ensembl Genes ENSG00000199377 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000362507 ENTREZGENE
GTEx ENSG00000199377 GTEx
HGNC ID HGNC:10216 ENTREZGENE
Human Proteome Map RNU5F-1 Human Proteome Map
NCBI Gene 26828 ENTREZGENE
OMIM 620363 OMIM
RNAcentral URS0000759ECB RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-01 RNU5F-1  RNA, U5F small nuclear 1  RNU5F  RNA, U5F small nuclear  Symbol and/or name change 5135510 APPROVED