MIR541 (microRNA 541) - Rat Genome Database
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Gene: MIR541 (microRNA 541) Homo sapiens
Analyze
Symbol: MIR541
Name: microRNA 541
RGD ID: 2290246
HGNC Page HGNC
Description: Predicted to be involved in long-term synaptic potentiation; negative regulation of gene expression; and type B pancreatic cell development.
Type: ncrna
RefSeq Status: PROVISIONAL
Also known as: hsa-mir-541; mir-541; MIRN541
RGD Orthologs
Mouse
Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14101,064,495 - 101,064,578 (+)EnsemblGRCh38hg38GRCh38
GRCh3814101,064,495 - 101,064,578 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714101,530,832 - 101,530,915 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614100,600,584 - 100,600,667 (+)NCBINCBI36hg18NCBI36
Celera1481,586,894 - 81,586,977 (+)NCBI
Cytogenetic Map14q32.31NCBI
HuRef1481,714,206 - 81,714,289 (+)NCBIHuRef
CHM1_114101,469,854 - 101,469,937 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process

References

Additional References at PubMed
PMID:16381832   PMID:17604727   PMID:21037258   PMID:23254460   PMID:23533592   PMID:25135278   PMID:27448300   PMID:29659195   PMID:30278884   PMID:31590696   PMID:31858539   PMID:32145546  


Genomics

Comparative Map Data
MIR541
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14101,064,495 - 101,064,578 (+)EnsemblGRCh38hg38GRCh38
GRCh3814101,064,495 - 101,064,578 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714101,530,832 - 101,530,915 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614100,600,584 - 100,600,667 (+)NCBINCBI36hg18NCBI36
Celera1481,586,894 - 81,586,977 (+)NCBI
Cytogenetic Map14q32.31NCBI
HuRef1481,714,206 - 81,714,289 (+)NCBIHuRef
CHM1_114101,469,854 - 101,469,937 (+)NCBICHM1_1
Mir541
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912109,708,843 - 109,708,932 (+)NCBIGRCm39mm39
GRCm39 Ensembl12109,708,843 - 109,708,932 (+)Ensembl
GRCm3812109,742,409 - 109,742,498 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12109,742,409 - 109,742,498 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712110,980,619 - 110,980,708 (+)NCBIGRCm37mm9NCBIm37
Celera12110,939,639 - 110,939,728 (+)NCBICelera
Cytogenetic Map12F1NCBI
Mir541
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26128,757,016 - 128,757,105 (+)NCBI
Rnor_6.0 Ensembl6133,892,655 - 133,892,744 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06133,892,655 - 133,892,744 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06143,055,012 - 143,055,101 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera6126,341,395 - 126,341,484 (+)NCBICelera
Cytogenetic Map6q32NCBI

miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:73022
Count of gene targets:22165
Count of transcripts:55530
Interacting mature miRNAs:hsa-miR-541-3p, hsa-miR-541-5p
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
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 adipose tissue appendage entire extraembryonic component
High
Medium 1 2 4 8 2 1 2 1
Low 20 11 50 12 22 11 34 28 94 3 59 35 2 9 7 1
Below cutoff 17 11 43 3 8 2 13 16 82 1 16 3 1 10 7

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000401360
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl14101,064,495 - 101,064,578 (+)Ensembl
RefSeq Acc Id: NR_030594
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3814101,064,495 - 101,064,578 (+)NCBI
GRCh3714101,530,832 - 101,530,915 (+)RGD
Celera1481,586,894 - 81,586,977 (+)RGD
HuRef1481,714,206 - 81,714,289 (+)ENTREZGENE
CHM1_114101,469,854 - 101,469,937 (+)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q32.2-32.33(chr14:99831655-106855263)x1 copy number loss See cases [RCV000133831] Chr14:99831655..106855263 [GRCh38]
Chr14:100297992..107263478 [GRCh37]
Chr14:99367745..106334523 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:73655772-106879298)x3 copy number gain See cases [RCV000134000] Chr14:73655772..106879298 [GRCh38]
Chr14:74122475..107287505 [GRCh37]
Chr14:73192228..106358550 [NCBI36]
Chr14:14q24.3-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97638520-106855263)x3 copy number gain See cases [RCV000135400] Chr14:97638520..106855263 [GRCh38]
Chr14:98104857..107263478 [GRCh37]
Chr14:97174610..106334523 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100309382-105987610)x3 copy number gain See cases [RCV000135410] Chr14:100309382..105987610 [GRCh38]
Chr14:100775719..106453697 [GRCh37]
Chr14:99845472..105524742 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:99448012-106850609)x3 copy number gain See cases [RCV000135875] Chr14:99448012..106850609 [GRCh38]
Chr14:99914349..107258824 [GRCh37]
Chr14:98984102..106329869 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33
pathogenic
GRCh38/hg38 14q32.12-32.33(chr14:92540983-104863658)x3 copy number gain See cases [RCV000135896] Chr14:92540983..104863658 [GRCh38]
Chr14:93007328..105329995 [GRCh37]
Chr14:92077081..104401040 [NCBI36]
Chr14:14q32.12-32.33
pathogenic
GRCh38/hg38 14q32.13-32.33(chr14:95524407-106879501)x1 copy number loss See cases [RCV000136032] Chr14:95524407..106879501 [GRCh38]
Chr14:95990744..107287708 [GRCh37]
Chr14:95060497..106358753 [NCBI36]
Chr14:14q32.13-32.33
pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:77222795-106879298)x3 copy number gain See cases [RCV000138230] Chr14:77222795..106879298 [GRCh38]
Chr14:77689138..107287505 [GRCh37]
Chr14:76758891..106358550 [NCBI36]
Chr14:14q24.3-32.33
pathogenic
GRCh38/hg38 14q32.2-32.31(chr14:100262836-102500697)x1 copy number loss See cases [RCV000139723] Chr14:100262836..102500697 [GRCh38]
Chr14:100729173..102967034 [GRCh37]
Chr14:99798926..102036787 [NCBI36]
Chr14:14q32.2-32.31
pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100582059-106877229)x1 copy number loss See cases [RCV000143662] Chr14:100582059..106877229 [GRCh38]
Chr14:101048396..107285437 [GRCh37]
Chr14:100118149..106356482 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
NC_000014.9:g.100806482_101281031del474550 deletion Paternal uniparental disomy of chromosome 14 [RCV000149429] Chr14:100806482..101281031 [GRCh38]
Chr14:101272819..101747368 [GRCh37]
Chr14:14q32.2-32.31
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100590353-106855264)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051553]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051553]|See cases [RCV000051553] Chr14:100590353..106855264 [GRCh38]
Chr14:101056690..107263479 [GRCh37]
Chr14:100126443..106334524 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97938637-106855263)x1 copy number loss See cases [RCV000050696] Chr14:97938637..106855263 [GRCh38]
Chr14:98404974..107263478 [GRCh37]
Chr14:97474727..106334523 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100309382-106855263)x1 copy number loss See cases [RCV000050938] Chr14:100309382..106855263 [GRCh38]
Chr14:100775719..107263478 [GRCh37]
Chr14:99845472..106334523 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100808300-106855263)x1 copy number loss See cases [RCV000051113] Chr14:100808300..106855263 [GRCh38]
Chr14:101274637..107263478 [GRCh37]
Chr14:100344390..106334523 [NCBI36]
Chr14:14q32.2-32.33
pathogenic
GRCh38/hg38 14q31.2-32.33(chr14:83912345-106855405)x3 copy number gain See cases [RCV000052294] Chr14:83912345..106855405 [GRCh38]
Chr14:84378689..107263620 [GRCh37]
Chr14:83448442..106334665 [NCBI36]
Chr14:14q31.2-32.33
pathogenic
GRCh38/hg38 14q31.3-32.33(chr14:86094030-106832642)x3 copy number gain See cases [RCV000052295] Chr14:86094030..106832642 [GRCh38]
Chr14:86560374..107240869 [GRCh37]
Chr14:85630127..106311914 [NCBI36]
Chr14:14q31.3-32.33
pathogenic
GRCh38/hg38 14q32.12-32.33(chr14:91455861-106832642)x3 copy number gain See cases [RCV000052296] Chr14:91455861..106832642 [GRCh38]
Chr14:91922205..107240869 [GRCh37]
Chr14:90991958..106311914 [NCBI36]
Chr14:14q32.12-32.33
pathogenic
GRCh38/hg38 14q32.13-32.33(chr14:94628219-106451054)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052298]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052298]|See cases [RCV000052298] Chr14:94628219..106451054 [GRCh38]
Chr14:95094556..106906960 [GRCh37]
Chr14:94164309..105978005 [NCBI36]
Chr14:14q32.13-32.33
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:33650 AgrOrtholog
COSMIC MIR541 COSMIC
Ensembl Genes ENSG00000216179 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000401360 ENTREZGENE
GTEx ENSG00000216179 GTEx
HGNC ID HGNC:33650 ENTREZGENE
Human Proteome Map MIR541 Human Proteome Map
miRBase MI0005539 ENTREZGENE
NCBI Gene 100126308 ENTREZGENE
PharmGKB PA164722812 PharmGKB
RNAcentral URS0000076E54 RNACentral
  URS000075A3AC RNACentral
  URS000075BC5F RNACentral