RNU4-1 (RNA, U4 small nuclear 1) - Rat Genome Database

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Gene: RNU4-1 (RNA, U4 small nuclear 1) Homo sapiens
Analyze
Symbol: RNU4-1
Name: RNA, U4 small nuclear 1
RGD ID: 1342825
HGNC Page HGNC:10192
Description: Predicted to enable U6 snRNA binding activity. 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 snRNP and U4/U6 x U5 tri-snRNP complex; INTERACTS WITH doxorubicin; perfluorooctanoic acid; picene.
Type: snrna
RefSeq Status: PROVISIONAL
Previously known as: RNA, U4A small nuclear; rna, u4b2 small nuclear; RNU4A; RNU4B2; U4; U4BL
RGD Orthologs
Mouse
Rat
Dog
Alliance Orthologs
More Info more info ...
Related Pseudogenes: RNU4-11P   RNU4-12P   RNU4-13P   RNU4-14P   RNU4-15P   RNU4-16P   RNU4-17P   RNU4-18P   RNU4-20P   RNU4-21P   RNU4-22P   RNU4-23P   RNU4-24P   RNU4-25P   RNU4-26P   RNU4-27P   RNU4-28P   RNU4-29P   RNU4-30P   RNU4-31P   RNU4-32P   RNU4-33P   RNU4-34P   RNU4-35P   RNU4-36P   RNU4-37P   RNU4-38P   RNU4-39P   RNU4-40P   RNU4-41P   RNU4-42P   RNU4-43P   RNU4-44P   RNU4-45P   RNU4-46P   RNU4-47P   RNU4-48P   RNU4-49P   RNU4-4P   RNU4-50P   RNU4-51P   RNU4-52P   RNU4-53P   RNU4-54P   RNU4-55P   RNU4-56P   RNU4-57P   RNU4-58P   RNU4-59P   RNU4-60P   RNU4-61P   RNU4-62P   RNU4-63P   RNU4-64P   RNU4-65P   RNU4-66P   RNU4-67P   RNU4-68P   RNU4-69P   RNU4-70P   RNU4-71P   RNU4-72P   RNU4-73P   RNU4-74P   RNU4-75P   RNU4-76P   RNU4-77P   RNU4-78P   RNU4-79P   RNU4-80P   RNU4-81P   RNU4-82P   RNU4-83P   RNU4-84P   RNU4-85P   RNU4-86P   RNU4-87P   RNU4-88P   RNU4-89P   RNU4-90P   RNU4-91P   RNU4-92P   RNU4-9P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812120,293,094 - 120,293,237 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12120,293,097 - 120,293,237 (-)EnsemblGRCh38hg38GRCh38
GRCh3712120,730,897 - 120,731,040 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612119,215,280 - 119,215,423 (-)NCBINCBI36Build 36hg18NCBI36
Celera12120,364,011 - 120,364,154 (-)NCBICelera
Cytogenetic Map12q24.23NCBI
HuRef12117,739,169 - 117,739,312 (-)NCBIHuRef
CHM1_112120,698,893 - 120,699,036 (-)NCBICHM1_1
T2T-CHM13v2.012120,280,271 - 120,280,414 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (HEP)

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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Xiong Y, etal., Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.
Additional References at PubMed
PMID:2176635   PMID:3582982   PMID:6169000   PMID:9847074   PMID:12384583   PMID:14691257   PMID:17332742   PMID:17632523   PMID:23221635   PMID:24796696   PMID:25263594   PMID:26275778  
PMID:29117863   PMID:30165668  


Genomics

Comparative Map Data
RNU4-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812120,293,094 - 120,293,237 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12120,293,097 - 120,293,237 (-)EnsemblGRCh38hg38GRCh38
GRCh3712120,730,897 - 120,731,040 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612119,215,280 - 119,215,423 (-)NCBINCBI36Build 36hg18NCBI36
Celera12120,364,011 - 120,364,154 (-)NCBICelera
Cytogenetic Map12q24.23NCBI
HuRef12117,739,169 - 117,739,312 (-)NCBIHuRef
CHM1_112120,698,893 - 120,699,036 (-)NCBICHM1_1
T2T-CHM13v2.012120,280,271 - 120,280,414 (-)NCBIT2T-CHM13v2.0
Gm24265
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395115,627,518 - 115,627,658 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5115,627,518 - 115,627,658 (+)EnsemblGRCm39 Ensembl
GRCm385115,489,459 - 115,489,599 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5115,489,459 - 115,489,599 (+)EnsemblGRCm38mm10GRCm38
Cytogenetic Map5FNCBI
LOC120096085
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81246,786,790 - 46,786,930 (-)NCBIGRCr8
mRatBN7.21241,126,050 - 41,126,190 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1241,126,050 - 41,126,190 (-)EnsemblmRatBN7.2 Ensembl
Cytogenetic Map12q16NCBI
LOC119866294
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2616,228,368 - 16,228,508 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02616,491,978 - 16,492,118 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2616,491,978 - 16,492,118 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12616,452,724 - 16,452,864 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02616,529,802 - 16,529,942 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02616,571,039 - 16,571,179 (-)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12q24.21-24.33(chr12:114268403-133201316)x3 copy number gain See cases [RCV000143656] Chr12:114268403..133201316 [GRCh38]
Chr12:114706208..133777902 [GRCh37]
Chr12:113190591..132287975 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:118165459-133182322)x3 copy number gain See cases [RCV000050866] Chr12:118165459..133182322 [GRCh38]
Chr12:118603264..133758908 [GRCh37]
Chr12:117087647..132268981 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.31(chr12:119286893-122638552)x3 copy number gain See cases [RCV000051981] Chr12:119286893..122638552 [GRCh38]
Chr12:119724698..123123099 [GRCh37]
Chr12:118209081..121689052 [NCBI36]
Chr12:12q24.23-24.31		 uncertain significance
GRCh38/hg38 12q24.21-24.33(chr12:115131583-133166920)x3 copy number gain See cases [RCV000053689] Chr12:115131583..133166920 [GRCh38]
Chr12:115569388..133743506 [GRCh37]
Chr12:114053771..132253579 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:119417382-133191400)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|See cases [RCV000053691] Chr12:119417382..133191400 [GRCh38]
Chr12:119855187..133767986 [GRCh37]
Chr12:118339570..132278059 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:111
Interacting mature miRNAs:112
Transcripts:ENST00000363925
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 9 1 16 1 1 2
Medium 26 6 18 7 69 6 6 7 31 4 71 19 3 1 2 1
Low 597 678 610 227 903 180 939 260 954 194 728 620 53 309 458 3 2
Below cutoff 531 538 313 129 218 91 720 392 671 64 135 246 40 218 489

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000363925
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12120,293,097 - 120,293,237 (-)Ensembl
RefSeq Acc Id: NR_003925
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812120,293,094 - 120,293,237 (-)NCBI
GRCh3712120,730,897 - 120,731,040 (-)RGD
Build 3612119,215,280 - 119,215,423 (-)NCBI Archive
Celera12120,364,011 - 120,364,154 (-)RGD
HuRef12117,739,169 - 117,739,312 (-)RGD
CHM1_112120,698,893 - 120,699,036 (-)NCBI
T2T-CHM13v2.012120,280,271 - 120,280,414 (-)NCBI
Sequence:
Promoters
RGD ID:6789993
Promoter ID:HG_KWN:16820
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000363925
Position:
Human AssemblyChrPosition (strand)Source
Build 3612119,215,026 - 119,215,526 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC RNU4-1 COSMIC
Ensembl Genes ENSG00000200795 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000363925 ENTREZGENE
GTEx ENSG00000200795 GTEx
HGNC ID HGNC:10192 ENTREZGENE
Human Proteome Map RNU4-1 Human Proteome Map
NCBI Gene 26835 ENTREZGENE
OMIM 620822 OMIM
PharmGKB PA34559 PharmGKB
RNAcentral URS00003F07BD RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-05 RNU4-1  RNA, U4 small nuclear 1  RNU4A  RNA, U4A small nuclear  Data merged from RGD:1347384 737654 PROVISIONAL