MIR3138 (microRNA 3138) - Rat Genome Database

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Gene: MIR3138 (microRNA 3138) Homo sapiens
Analyze
Symbol: MIR3138
Name: microRNA 3138
RGD ID: 4108890
HGNC Page HGNC:38341
Description: microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: mir-3138
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38410,078,611 - 10,078,692 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl410,078,611 - 10,078,692 (-)EnsemblGRCh38hg38GRCh38
GRCh37410,080,235 - 10,080,316 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera410,562,601 - 10,562,682 (-)NCBICelera
Cytogenetic Map4p16.1NCBI
HuRef49,413,985 - 9,414,066 (-)NCBIHuRef
CHM1_1410,078,391 - 10,078,472 (-)NCBICHM1_1
T2T-CHM13v2.0410,078,197 - 10,078,278 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16381832   PMID:20224791   PMID:20300190   PMID:21037258   PMID:26698155   PMID:33509040  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4p16.3-14(chr4:72555-39477144)x3 copy number gain See cases [RCV000133677] Chr4:72555..39477144 [GRCh38]
Chr4:72447..39478764 [GRCh37]
Chr4:62447..39155159 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p16.3-16.1(chr4:78578-10335613)x1 copy number loss See cases [RCV000135336] Chr4:78578..10335613 [GRCh38]
Chr4:78470..10337237 [GRCh37]
Chr4:68470..9946335 [NCBI36]
Chr4:4p16.3-16.1		 pathogenic
GRCh38/hg38 4p16.3-15.32(chr4:78578-15625573)x3 copy number gain See cases [RCV000135349] Chr4:78578..15625573 [GRCh38]
Chr4:78470..15627196 [GRCh37]
Chr4:68470..15236294 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.3-15.32(chr4:72555-17278013)x1 copy number loss See cases [RCV000135657] Chr4:72555..17278013 [GRCh38]
Chr4:72447..17279636 [GRCh37]
Chr4:62447..16888734 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.3-15.32(chr4:72555-15658035)x1 copy number loss See cases [RCV000135532] Chr4:72555..15658035 [GRCh38]
Chr4:72447..15659658 [GRCh37]
Chr4:62447..15268756 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.1(chr4:9813220-10817946)x3 copy number gain See cases [RCV000136068] Chr4:9813220..10817946 [GRCh38]
Chr4:9814844..10819570 [GRCh37]
Chr4:9423942..10428668 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.3-16.1(chr4:72555-10250666)x1 copy number loss See cases [RCV000137036] Chr4:72555..10250666 [GRCh38]
Chr4:72447..10252290 [GRCh37]
Chr4:62447..9861388 [NCBI36]
Chr4:4p16.3-16.1		 pathogenic|uncertain significance
GRCh38/hg38 4p16.3-15.31(chr4:51519-17798196)x3 copy number gain See cases [RCV000137071] Chr4:51519..17798196 [GRCh38]
Chr4:51413..17799819 [GRCh37]
Chr4:41413..17408917 [NCBI36]
Chr4:4p16.3-15.31		 pathogenic
GRCh38/hg38 4p16.3-12(chr4:36424-47491595)x3 copy number gain See cases [RCV000137261] Chr4:36424..47491595 [GRCh38]
Chr4:36424..47493612 [GRCh37]
Chr4:26424..47188369 [NCBI36]
Chr4:4p16.3-12		 pathogenic
GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1 copy number loss See cases [RCV000138198] Chr4:72555..12898612 [GRCh38]
Chr4:72447..12900236 [GRCh37]
Chr4:62447..12509334 [NCBI36]
Chr4:4p16.3-15.33		 pathogenic
GRCh38/hg38 4p16.1(chr4:9813220-11009701)x3 copy number gain See cases [RCV000138398] Chr4:9813220..11009701 [GRCh38]
Chr4:9814844..11011325 [GRCh37]
Chr4:9423942..10620423 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.3-15.31(chr4:72555-21022414)x3 copy number gain See cases [RCV000138305] Chr4:72555..21022414 [GRCh38]
Chr4:72447..21024037 [GRCh37]
Chr4:62447..20633135 [NCBI36]
Chr4:4p16.3-15.31		 pathogenic
GRCh38/hg38 4p16.1(chr4:9813097-10873771)x3 copy number gain See cases [RCV000140423] Chr4:9813097..10873771 [GRCh38]
Chr4:9814721..10875395 [GRCh37]
Chr4:9423819..10484493 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.3-15.32(chr4:37335-15869056)x1 copy number loss See cases [RCV000139551] Chr4:37335..15869056 [GRCh38]
Chr4:37336..15870679 [GRCh37]
Chr4:27336..15479777 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.3-15.32(chr4:4426403-17460549)x1 copy number loss See cases [RCV000141502] Chr4:4426403..17460549 [GRCh38]
Chr4:4428130..17462172 [GRCh37]
Chr4:4479031..17071270 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.1(chr4:9846063-10651440)x3 copy number gain See cases [RCV000142152] Chr4:9846063..10651440 [GRCh38]
Chr4:9847687..10653064 [GRCh37]
Chr4:9456785..10262162 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.1(chr4:9369290-10250666)x3 copy number gain See cases [RCV000142611] Chr4:9369290..10250666 [GRCh38]
Chr4:9371016..10252290 [GRCh37]
Chr4:8980114..9861388 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.1(chr4:9500007-10147031)x3 copy number gain See cases [RCV000143287] Chr4:9500007..10147031 [GRCh38]
Chr4:9501651..10148655 [GRCh37]
Chr4:9110749..9757753 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.1(chr4:9813097-10714839)x3 copy number gain See cases [RCV000143145] Chr4:9813097..10714839 [GRCh38]
Chr4:9814721..10716463 [GRCh37]
Chr4:9423819..10325561 [NCBI36]
Chr4:4p16.1		 likely benign|uncertain significance
GRCh38/hg38 4p16.3-15.33(chr4:68453-14612453)x1 copy number loss See cases [RCV000143686] Chr4:68453..14612453 [GRCh38]
Chr4:68345..14614077 [GRCh37]
Chr4:58345..14223175 [NCBI36]
Chr4:4p16.3-15.33		 pathogenic
GRCh38/hg38 4p16.3-15.31(chr4:68453-20385608)x1 copy number loss See cases [RCV000143713] Chr4:68453..20385608 [GRCh38]
Chr4:68345..20387231 [GRCh37]
Chr4:58345..19996329 [NCBI36]
Chr4:4p16.3-15.31		 pathogenic
GRCh38/hg38 4p16.3-15.33(chr4:56878-14499760)x1 copy number loss See cases [RCV000051614] Chr4:56878..14499760 [GRCh38]
Chr4:56772..14501384 [GRCh37]
Chr4:46772..14110482 [NCBI36]
Chr4:4p16.3-15.33		 pathogenic
GRCh38/hg38 4p16.3-15.33(chr4:72555-11610824)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051674]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051674]|See cases [RCV000051674] Chr4:72555..11610824 [GRCh38]
Chr4:72447..11612448 [GRCh37]
Chr4:62447..11221546 [NCBI36]
Chr4:4p16.3-15.33		 pathogenic
GRCh38/hg38 4p16.1(chr4:10011787-10873830)x3 copy number gain See cases [RCV000137872] Chr4:10011787..10873830 [GRCh38]
Chr4:10013411..10875454 [GRCh37]
Chr4:9622509..10484552 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.3-16.1(chr4:51319-10250807)x3 copy number gain See cases [RCV000051743] Chr4:51319..10250807 [GRCh38]
Chr4:51213..10252431 [GRCh37]
Chr4:41213..9861529 [NCBI36]
Chr4:4p16.3-16.1		 pathogenic
GRCh38/hg38 4p16.3-15.1(chr4:72555-28066309)x1 copy number loss See cases [RCV000051642] Chr4:72555..28066309 [GRCh38]
Chr4:72447..28067931 [GRCh37]
Chr4:62447..27677029 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-15.2(chr4:51519-26519788)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051752]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051752]|See cases [RCV000051752] Chr4:51519..26519788 [GRCh38]
Chr4:51413..26521410 [GRCh37]
Chr4:41413..26130508 [NCBI36]
Chr4:4p16.3-15.2		 pathogenic
GRCh38/hg38 4p16.3-15.1(chr4:72555-33130620)x3 copy number gain See cases [RCV000051753] Chr4:72555..33130620 [GRCh38]
Chr4:72447..33132242 [GRCh37]
Chr4:62447..32808637 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-15.2(chr4:85149-22450018)x3 copy number gain See cases [RCV000051755] Chr4:85149..22450018 [GRCh38]
Chr4:85040..22451641 [GRCh37]
Chr4:75040..22060739 [NCBI36]
Chr4:4p16.3-15.2		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:85149-38700366)x3 copy number gain See cases [RCV000051757] Chr4:85149..38700366 [GRCh38]
Chr4:85040..38701987 [GRCh37]
Chr4:75040..38378382 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p16.3-15.32(chr4:85149-17486742)x1 copy number loss See cases [RCV000051679] Chr4:85149..17486742 [GRCh38]
Chr4:85040..17488365 [GRCh37]
Chr4:75040..17097463 [NCBI36]
Chr4:4p16.3-15.32		 pathogenic
GRCh38/hg38 4p16.3-16.1(chr4:2231690-11197847)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051758]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051758]|See cases [RCV000051758] Chr4:2231690..11197847 [GRCh38]
Chr4:2233417..11199471 [GRCh37]
Chr4:2203215..10808569 [NCBI36]
Chr4:4p16.3-16.1		 pathogenic
GRCh38/hg38 4p16.1(chr4:9946194-10938417)x3 copy number gain See cases [RCV000051759] Chr4:9946194..10938417 [GRCh38]
Chr4:9947818..10940041 [GRCh37]
Chr4:9556916..10549139 [NCBI36]
Chr4:4p16.1		 pathogenic
GRCh38/hg38 4p16.1(chr4:9381969-10163409)x3 copy number gain See cases [RCV000051567] Chr4:9381969..10163409 [GRCh38]
Chr4:9383695..10165033 [GRCh37]
Chr4:8992793..9774131 [NCBI36]
Chr4:4p16.1		 uncertain significance
GRCh38/hg38 4p16.2-16.1(chr4:5455628-10640216)x1 copy number loss See cases [RCV000053262] Chr4:5455628..10640216 [GRCh38]
Chr4:5457355..10641840 [GRCh37]
Chr4:5508256..10250938 [NCBI36]
Chr4:4p16.2-16.1		 pathogenic
NC_000004.12:g.8398067_17505522inv inversion Dihydropteridine reductase deficiency [RCV000768549] Chr4:8398067..17505522 [GRCh38]
Chr4:4p16.1-15.32		 pathogenic
GRCh38/hg38 4p16.3-11(chr4:1-49062177)x3 copy number gain Neurodevelopmental disorder [RCV003327611] Chr4:1..49062177 [GRCh38]
Chr4:4p16.3-11		 pathogenic
GRCh38/hg38 4p16.3-13(chr4:2904667-42963232)x3 copy number gain Neurodevelopmental disorder [RCV003327612] Chr4:2904667..42963232 [GRCh38]
Chr4:4p16.3-13		 pathogenic
GRCh38/hg38 4p16.3-q12(chr4:85624-57073230)x3 copy number gain Neurodevelopmental disorder [RCV003327613] Chr4:85624..57073230 [GRCh38]
Chr4:4p16.3-q12		 pathogenic
GRCh38/hg38 4p16.1(chr4:9946394-10449826)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054038]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054038]|See cases [RCV000054038] Chr4:9946394..10449826 [GRCh38]
Chr4:9948018..10451450 [GRCh37]
Chr4:9557116..10060548 [NCBI36]
Chr4:4p16.1		 uncertain significance
miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:22032
Count of gene targets:9048
Count of transcripts:17264
Interacting mature miRNAs:hsa-miR-3138
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 1 2 1 10 1 2 1
Low 217 164 245 106 339 99 307 97 171 110 259 328 18 98 132 3
Below cutoff 132 129 73 27 69 14 144 90 88 28 78 67 13 69 74

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000585238
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl410,078,611 - 10,078,692 (-)Ensembl
RefSeq Acc Id: NR_036090
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38410,078,611 - 10,078,692 (-)NCBI
GRCh37410,080,235 - 10,080,316 (-)RGD
Celera410,562,601 - 10,562,682 (-)RGD
HuRef49,413,985 - 9,414,066 (-)RGD
CHM1_1410,078,391 - 10,078,472 (-)NCBI
T2T-CHM13v2.0410,078,197 - 10,078,278 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR3138 COSMIC
Ensembl Genes ENSG00000264931 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000585238 ENTREZGENE
GTEx ENSG00000264931 GTEx
HGNC ID HGNC:38341 ENTREZGENE
Human Proteome Map MIR3138 Human Proteome Map
miRBase MI0014161 ENTREZGENE
NCBI Gene 100423011 ENTREZGENE
PharmGKB PA165664219 PharmGKB
RNAcentral URS00002C83DA RNACentral
  URS000075E93A RNACentral