MIR548XHG (MIR548X host gene) - Rat Genome Database

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Gene: MIR548XHG (MIR548X host gene) Homo sapiens
Analyze
Symbol: MIR548XHG
Name: MIR548X host gene
RGD ID: 10402702
HGNC Page HGNC:52006
Description: INTERACTS WITH aflatoxin B1
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382118,561,265 - 18,759,812 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2118,561,265 - 18,760,320 (-)EnsemblGRCh38hg38GRCh38
GRCh372119,933,583 - 20,132,130 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map21q21.1NCBI
HuRef215,321,490 - 5,519,971 (-)NCBIHuRef
CHM1_12119,494,614 - 19,693,182 (-)NCBICHM1_1
T2T-CHM13v2.02116,920,895 - 17,119,428 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
aflatoxin B1  (EXP)

References
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in MIR548XHG
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 21q21.1(chr21:18623576-20834883)x1 copy number loss See cases [RCV000138298] Chr21:18623576..20834883 [GRCh38]
Chr21:19995894..22207201 [GRCh37]
Chr21:18917765..21129072 [NCBI36]
Chr21:21q21.1		 pathogenic|likely benign
GRCh38/hg38 21q11.2-21.1(chr21:14112717-21297273)x1 copy number loss See cases [RCV000138781] Chr21:14112717..21297273 [GRCh38]
Chr21:15485038..22669593 [GRCh37]
Chr21:14406909..21591464 [NCBI36]
Chr21:21q11.2-21.1		 pathogenic
GRCh38/hg38 21q11.2-21.3(chr21:13634137-27862841)x1 copy number loss See cases [RCV000143749] Chr21:13634137..27862841 [GRCh38]
Chr21:15006458..29235160 [GRCh37]
Chr21:13928329..28157031 [NCBI36]
Chr21:21q11.2-21.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053039] Chr21:7749532..46623792 [GRCh38]
Chr21:14524963..48043704 [GRCh37]
Chr21:13446834..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46653090)x3 copy number gain See cases [RCV000053040] Chr21:7749532..46653090 [GRCh38]
Chr21:14539679..48073002 [GRCh37]
Chr21:13461550..46897430 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053042] Chr21:7749532..46623792 [GRCh38]
Chr21:14595524..48043704 [GRCh37]
Chr21:13517395..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053043] Chr21:7749532..46623792 [GRCh38]
Chr21:14629063..48043704 [GRCh37]
Chr21:13550934..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670546)x3 copy number gain See cases [RCV000053045] Chr21:7749532..46670546 [GRCh38]
Chr21:15499647..48090458 [GRCh37]
Chr21:14421518..46914886 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053065] Chr21:7749532..46661140 [GRCh38]
Chr21:15499647..48081052 [GRCh37]
Chr21:14421518..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053067] Chr21:7749532..46661140 [GRCh38]
Chr21:15499847..48081052 [GRCh37]
Chr21:14421718..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000053068] Chr21:7749532..46670405 [GRCh38]
Chr21:20655360..48090317 [GRCh37]
Chr21:19577231..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000053069] Chr21:7749532..46670405 [GRCh38]
Chr21:34423268..48090317 [GRCh37]
Chr21:33345138..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-42971047)x3 copy number gain See cases [RCV000133676] Chr21:7749532..42971047 [GRCh38]
Chr21:15499847..44391157 [GRCh37]
Chr21:14421718..43264226 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670440)x3 copy number gain See cases [RCV000134119] Chr21:7749532..46670440 [GRCh38]
Chr21:15485038..48090352 [GRCh37]
Chr21:14406909..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46649831)x3 copy number gain See cases [RCV000134509] Chr21:7749532..46649831 [GRCh38]
Chr21:14577835..48069743 [GRCh37]
Chr21:13499706..46894171 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46653084)x3 copy number gain See cases [RCV000134727] Chr21:7749532..46653084 [GRCh38]
Chr21:15485038..48072996 [GRCh37]
Chr21:14406909..46897424 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46664250)x3 copy number gain See cases [RCV000134836] Chr21:7749532..46664250 [GRCh38]
Chr21:15485038..48084162 [GRCh37]
Chr21:14406909..46908590 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670440)x3 copy number gain See cases [RCV000134842] Chr21:7749532..46670440 [GRCh38]
Chr21:15513244..48090352 [GRCh37]
Chr21:14435115..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q22.11-22.3(chr21:7749532-46670346)x3 copy number gain See cases [RCV000135310] Chr21:7749532..46670346 [GRCh38]
Chr21:34111831..48090258 [GRCh37]
Chr21:33033702..46914686 [NCBI36]
Chr21:21q22.11-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46660999)x3 copy number gain See cases [RCV000135448] Chr21:7749532..46660999 [GRCh38]
Chr21:15499847..48080911 [GRCh37]
Chr21:14421718..46905339 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000137255] Chr21:7749532..46671060 [GRCh38]
Chr21:35319225..48090972 [GRCh37]
Chr21:34241095..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000137337] Chr21:7749532..46671060 [GRCh38]
Chr21:10697897..48090972 [GRCh37]
Chr21:1..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.13(chr21:7749532-37653653)x1 copy number loss See cases [RCV000138095] Chr21:7749532..37653653 [GRCh38]
Chr21:15451032..39025955 [GRCh37]
Chr21:14372903..37947825 [NCBI36]
Chr21:21p11.2-q22.13		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000138216] Chr21:7749532..46671060 [GRCh38]
Chr21:10944001..48090972 [GRCh37]
Chr21:9965872..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46671060)x3 copy number gain See cases [RCV000138436] Chr21:7749532..46671060 [GRCh38]
Chr21:15451032..48090972 [GRCh37]
Chr21:14372903..46915400 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46670346)x3 copy number gain See cases [RCV000140103] Chr21:7749532..46670346 [GRCh38]
Chr21:14577894..48090258 [GRCh37]
Chr21:13499765..46914686 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46698247)x3 copy number gain See cases [RCV000141346] Chr21:7749532..46698247 [GRCh38]
Chr21:14577835..48118159 [GRCh37]
Chr21:13499706..46942587 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21q21.3-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000141827] Chr21:7749532..46677460 [GRCh38]
Chr21:28285299..48097372 [GRCh37]
Chr21:27207170..46921800 [NCBI36]
Chr21:21q21.3-22.3		 uncertain significance
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000143120] Chr21:7749532..46677460 [GRCh38]
Chr21:15006457..48097372 [GRCh37]
Chr21:13928328..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460) copy number gain See cases [RCV000143160] Chr21:7749532..46677460 [GRCh38]
Chr21:14386013..48097372 [GRCh37]
Chr21:13307884..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21q11.2-22.3(chr21:7749532-46677460)x3 copy number gain See cases [RCV000143376] Chr21:7749532..46677460 [GRCh38]
Chr21:15006458..48097372 [GRCh37]
Chr21:13928329..46921800 [NCBI36]
Chr21:21q11.2-22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000148131] Chr21:7749532..46670405 [GRCh38]
Chr21:15499847..48090317 [GRCh37]
Chr21:14421718..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000050445] Chr21:7749532..46670405 [GRCh38]
Chr21:15499847..48090317 [GRCh37]
Chr21:14421718..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 21q11.2-22.11(chr21:14000720-30903065)x1 copy number loss See cases [RCV000052799] Chr21:14000720..30903065 [GRCh38]
Chr21:15373041..32275384 [GRCh37]
Chr21:14294912..31197255 [NCBI36]
Chr21:21q11.2-22.11		 pathogenic
GRCh38/hg38 21q11.2-21.1(chr21:14127526-19238720)x1 copy number loss See cases [RCV000052801] Chr21:14127526..19238720 [GRCh38]
Chr21:15499847..20611037 [GRCh37]
Chr21:14421718..19532908 [NCBI36]
Chr21:21q11.2-21.1		 pathogenic
GRCh38/hg38 21q11.2-21.1(chr21:13076061-19390260)x3 copy number gain See cases [RCV000053038] Chr21:13076061..19390260 [GRCh38]
Chr21:14448382..20762577 [GRCh37]
Chr21:13370253..19684448 [NCBI36]
Chr21:21q11.2-21.1		 pathogenic
GRCh38/hg38 21q11.2-21.1(chr21:13696993-21440046)x3 copy number gain See cases [RCV000053044] Chr21:13696993..21440046 [GRCh38]
Chr21:15069314..22812366 [GRCh37]
Chr21:13991185..21734237 [NCBI36]
Chr21:21q11.2-21.1		 pathogenic
GRCh38/hg38 21q21.1-21.2(chr21:16872635-24024990)x3 copy number gain See cases [RCV000135653] Chr21:16872635..24024990 [GRCh38]
Chr21:18244955..25397305 [GRCh37]
Chr21:17166826..24319176 [NCBI36]
Chr21:21q21.1-21.2		 uncertain significance
GRCh38/hg38 21q21.1-21.2(chr21:15341716-22826315)x1 copy number loss See cases [RCV000136931] Chr21:15341716..22826315 [GRCh38]
Chr21:16714035..24198636 [GRCh37]
Chr21:15635906..23120507 [NCBI36]
Chr21:21q21.1-21.2		 pathogenic
GRCh38/hg38 21q11.2-21.3(chr21:13194345-29257208)x1 copy number loss See cases [RCV000052798] Chr21:13194345..29257208 [GRCh38]
Chr21:14566666..30629529 [GRCh37]
Chr21:13488537..29551400 [NCBI36]
Chr21:21q11.2-21.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7817158-46670440)x1 copy number loss See cases [RCV000142427] Chr21:7817158..46670440 [GRCh38]
Chr21:15485038..48090352 [GRCh37]
Chr21:14406909..46914780 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985) copy number loss Monosomy 21 [RCV000225561] Chr21:14000146..27785985 [GRCh38]
Chr21:21q11.2-21.3		 pathogenic
GRCh38/hg38 21p11.2-q21.3(chr21:13048294-27532614) copy number loss Monosomy 21 [RCV000225452] Chr21:13048294..27532614 [GRCh38]
Chr21:21p11.2-q21.3		 pathogenic
Single allele deletion not provided [RCV002266744] Chr21:16244543..20363082 [GRCh38]
Chr21:21q21.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:263
Count of miRNA genes:239
Interacting mature miRNAs:247
Transcripts:ENST00000355189, ENST00000414582, ENST00000437492
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 adipose tissue appendage entire extraembryonic component
High
Medium 5 7 5 13 5 6 4 5 3 12 19 1
Low 39 1 45 31 103 32 95 25 47 24 87 118 5 2 2
Below cutoff 217 254 150 47 183 42 437 101 540 108 328 241 11 56 211 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000355189
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,561,615 - 18,759,804 (-)Ensembl
RefSeq Acc Id: ENST00000414582
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,612,062 - 18,753,028 (-)Ensembl
RefSeq Acc Id: ENST00000437492
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,561,265 - 18,759,822 (-)Ensembl
RefSeq Acc Id: ENST00000653218
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,588,869 - 18,760,320 (-)Ensembl
RefSeq Acc Id: ENST00000656413
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,611,810 - 18,760,027 (-)Ensembl
RefSeq Acc Id: ENST00000671206
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2118,561,265 - 18,760,315 (-)Ensembl
RefSeq Acc Id: NR_109925
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382118,561,265 - 18,759,812 (-)NCBI
CHM1_12119,494,614 - 19,693,182 (-)NCBI
T2T-CHM13v2.02116,920,895 - 17,119,428 (-)NCBI
Sequence:
Promoters
RGD ID:15097386
Promoter ID:EPDNEWNC_H2165
Type:initiation region
Name:MIR548XHG_1
Description:MIR548X host gene [Source:HGNC Symbol;Acc:HGNC:52006]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382118,759,827 - 18,759,887EPDNEWNC
RGD ID:15097385
Promoter ID:EPDNEWNC_H2166
Type:initiation region
Name:MIR548XHG_2
Description:MIR548X host gene [Source:HGNC Symbol;Acc:HGNC:52006]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382118,760,043 - 18,760,103EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC MIR548XHG COSMIC
Ensembl Genes ENSG00000224141 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000437492 ENTREZGENE
GTEx ENSG00000224141 GTEx
HGNC ID HGNC:52006 ENTREZGENE
Human Proteome Map MIR548XHG Human Proteome Map
NCBI Gene MIR548XHG ENTREZGENE
RNAcentral URS000075DA0F RNACentral