MIMT1 (MER1 repeat containing imprinted transcript 1) - Rat Genome Database

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Gene: MIMT1 (MER1 repeat containing imprinted transcript 1) Homo sapiens
Analyze
Symbol: MIMT1
Name: MER1 repeat containing imprinted transcript 1
RGD ID: 2299990
HGNC Page HGNC:33464
Description: INTERACTS WITH valproic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LINC00067; MER1 repeat containing imprinted transcript 1 (non-protein coding); MIM1; NCRNA00067
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381956,840,902 - 56,848,556 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1956,840,866 - 56,848,556 (+)EnsemblGRCh38hg38GRCh38
GRCh371957,352,270 - 57,359,924 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera1954,394,357 - 54,402,006 (+)NCBICelera
Cytogenetic Map19q13.43NCBI
HuRef1953,661,753 - 53,669,405 (+)NCBIHuRef
CHM1_11957,345,823 - 57,353,475 (+)NCBICHM1_1
T2T-CHM13v2.01959,935,970 - 59,943,623 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17509818   PMID:20801769   PMID:26417259   PMID:36727289  


Genomics

Variants

.
Variants in MIMT1
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q13.41-13.43(chr19:52612432-58581203)x3 copy number gain See cases [RCV000134174] Chr19:52612432..58581203 [GRCh38]
Chr19:53115685..59092570 [GRCh37]
Chr19:57807497..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52955056-58581203)x3 copy number gain See cases [RCV000134139] Chr19:52955056..58581203 [GRCh38]
Chr19:53458309..59092570 [GRCh37]
Chr19:58150121..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55550939-57031576)x1 copy number loss See cases [RCV000135287] Chr19:55550939..57031576 [GRCh38]
Chr19:56062305..57542944 [GRCh37]
Chr19:60754117..62234756 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50152520-58581203)x3 copy number gain See cases [RCV000135843] Chr19:50152520..58581203 [GRCh38]
Chr19:50655777..59092570 [GRCh37]
Chr19:55347589..63784382 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55048514-56972458)x3 copy number gain See cases [RCV000138139] Chr19:55048514..56972458 [GRCh38]
Chr19:55595687..57483826 [GRCh37]
Chr19:60251694..62175638 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52143873-58445521)x3 copy number gain See cases [RCV000142008] Chr19:52143873..58445521 [GRCh38]
Chr19:52647126..58956888 [GRCh37]
Chr19:57338938..63648700 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.43(chr19:56353449-58445521)x3 copy number gain See cases [RCV000141900] Chr19:56353449..58445521 [GRCh38]
Chr19:56864818..58956888 [GRCh37]
Chr19:61556630..63648700 [NCBI36]
Chr19:19q13.43		 uncertain significance
GRCh38/hg38 19q13.33-13.43(chr19:49907832-58557889)x3 copy number gain See cases [RCV000052925] Chr19:49907832..58557889 [GRCh38]
Chr19:50411089..59069256 [GRCh37]
Chr19:55102901..63761068 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:51141518-58539965)x3 copy number gain See cases [RCV000052926] Chr19:51141518..58539965 [GRCh38]
Chr19:51644775..59051332 [GRCh37]
Chr19:56336587..63743144 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55037146-56982033)x3 copy number gain See cases [RCV000142245] Chr19:55037146..56982033 [GRCh38]
Chr19:55548514..57493401 [GRCh37]
Chr19:60240326..62185213 [NCBI36]
Chr19:19q13.42-13.43		 uncertain significance
GRCh38/hg38 19q13.33-13.43(chr19:50191219-58535818)x3 copy number gain See cases [RCV000050883] Chr19:50191219..58535818 [GRCh38]
Chr19:50694476..59047185 [GRCh37]
Chr19:55386288..63738997 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.43(chr19:56363208-58581203)x3 copy number gain See cases [RCV000052927] Chr19:56363208..58581203 [GRCh38]
Chr19:56874577..59092570 [GRCh37]
Chr19:61566389..63784382 [NCBI36]
Chr19:19q13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:161
Count of miRNA genes:136
Interacting mature miRNAs:139
Transcripts:ENST00000597105, ENST00000599641
Prediction methods:Microtar, 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.

Markers in Region
RH35916  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371957,354,408 - 57,354,556UniSTSGRCh37
Build 361962,046,220 - 62,046,368RGDNCBI36
Celera1954,396,495 - 54,396,643RGD
Cytogenetic Map19q13.43UniSTS
HuRef1953,663,891 - 53,664,039UniSTS
GeneMap99-GB4 RH Map19284.01UniSTS
SGC35094  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371957,354,475 - 57,354,604UniSTSGRCh37
Build 361962,046,287 - 62,046,416RGDNCBI36
Celera1954,396,562 - 54,396,691RGD
Cytogenetic Map19q13.43UniSTS
HuRef1953,663,958 - 53,664,087UniSTS
GeneMap99-GB4 RH Map19284.08UniSTS
Whitehead-RH Map19370.1UniSTS
A009Y38  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371957,354,366 - 57,354,613UniSTSGRCh37
Build 361962,046,178 - 62,046,425RGDNCBI36
Celera1954,396,453 - 54,396,700RGD
Cytogenetic Map19q13.43UniSTS
HuRef1953,663,849 - 53,664,096UniSTS
GeneMap99-GB4 RH Map19283.91UniSTS
G32993  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371957,354,366 - 57,354,613UniSTSGRCh37
Celera1954,396,453 - 54,396,700UniSTS
Cytogenetic Map19q13.43UniSTS
HuRef1953,663,849 - 53,664,096UniSTS


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 4 12 99 1
Low 5 15 399 22 4 22 10 17 2139 21 527 13 6 4
Below cutoff 1398 1349 903 303 223 170 2262 911 1340 151 475 808 132 650 1470

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000597105
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,841,249 - 56,842,298 (+)Ensembl
RefSeq Acc Id: ENST00000599641
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,840,902 - 56,848,556 (+)Ensembl
RefSeq Acc Id: ENST00000652034
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,840,866 - 56,848,554 (+)Ensembl
RefSeq Acc Id: NR_024059
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381956,840,902 - 56,848,556 (+)NCBI
GRCh371957,352,270 - 57,359,922 (+)RGD
Celera1954,394,357 - 54,402,006 (+)RGD
HuRef1953,661,753 - 53,669,405 (+)ENTREZGENE
CHM1_11957,345,823 - 57,353,475 (+)NCBI
T2T-CHM13v2.01959,935,970 - 59,943,623 (+)NCBI
Sequence:
Promoters
RGD ID:15097255
Promoter ID:EPDNEWNC_H2082
Type:initiation region
Name:MIMT1_1
Description:MER1 repeat containing imprinted transcript 1 [Source:HGNCSymbol;Acc:HGNC:33464]
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
GRCh381956,840,892 - 56,840,952EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC MIMT1 COSMIC
Ensembl Genes ENSG00000268654 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000599641 ENTREZGENE
GTEx ENSG00000268654 GTEx
HGNC ID HGNC:33464 ENTREZGENE
Human Proteome Map MIMT1 Human Proteome Map
NCBI Gene 100073347 ENTREZGENE
OMIM 620407 OMIM
PharmGKB PA162395967 PharmGKB
RNAcentral URS0000CCDF8F RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 MIMT1  MER1 repeat containing imprinted transcript 1    MER1 repeat containing imprinted transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED