pre-miRNA Information
pre-miRNA hsa-mir-3179-1   
Genomic Coordinates chr16: 14901508 - 14901591
Description Homo sapiens miR-3179-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-2   
Genomic Coordinates chr16: 16300159 - 16300242
Description Homo sapiens miR-3179-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-3   
Genomic Coordinates chr16: 18411894 - 18411977
Description Homo sapiens miR-3179-3 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-3179-4   
Genomic Coordinates chr16: 18494493 - 18494576
Description Homo sapiens miR-3179-4 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-3179
Sequence 52| AGAAGGGGUGAAAUUUAAACGU |73
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1351100204 1 dbSNP
rs1398613616 4 dbSNP
rs1340262765 20 dbSNP
rs1229893475 21 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol GRINA   
Synonyms HNRGW, LFG1, NMDARA1, TMBIM3
Description glutamate ionotropic receptor NMDA type subunit associated protein 1
Transcript NM_000837   
Other Transcripts NM_001009184   
Expression
Putative miRNA Targets on GRINA
3'UTR of GRINA
(miRNA target sites are highlighted)
>GRINA|NM_000837|3'UTR
   1 CCGAGCTCCAGCTCGCTGTGCCCGCTCAGGTGGCACGGCTGGCCTGGACCCTGCCCCTGGCACGGCAGTGCCAGCTGTAC
  81 TTCCCCTCTCTCTTGTCCCCAGGCACAGCCTAGGGAAAAGGATGCCTCTCTCCAACCCTCCTGTATGTACACTGCAGATA
 161 CTTCCATTTGGACCCGCTGTGGCCACAGCATGGCCCCTTTAGTCCTCCCGCCCCCGCCAAGGGGCACCAAGGCCACGTTT
 241 CCGTGCCACCTCCTGTCTACTCATTGTTGCATGAGCCCTGTCTGCCAGCCCACCCCAGGGACTGGGGGCAGCACCAGGTC
 321 CCGGGGAGAGGGATTGAGCCAAGAGGTGAGGGTGCACGTCTTCCCTCCTGTCCCAGCTCCCCAGCCTGGCGTAGAGCACC
 401 CCTCCCCTCCCCCCCACCCCCCTGGAGTGCTGCCCTCTGGGGACATGCGGAGTGGGGGTCTTATCCCTGTGCTGAGCCCT
 481 GAGGGCAGAGAGGATGGCATGTTTCAGGGGAGGGGGAAGCCTTCCTCTCAATTTGTTGTCAGTGAAATTCCAATAAATGG
 561 GATTTGCTCTCTGCAAAAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' ugcaaauuuaaAGUGGGGAAGa 5'
                     | :||||||: 
Target 5' tggccacagcaTGGCCCCTTTa 3'
180 - 201 127.00 -9.50
2
miRNA  3' ugcaaAUUUAAAGUGGGGAAGa 5'
               ||:|   ||||||| | 
Target 5' tggcgTAGA--GCACCCCTCCc 3'
387 - 406 121.00 -14.70
3
miRNA  3' ugcaaAUUUAAAGUGGGGA-AGa 5'
               |: | ||  ||||| || 
Target 5' ccagcTGTACTT--CCCCTCTCt 3'
71 - 91 113.00 -9.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30499644 2 COSMIC
COSN15667602 25 COSMIC
COSN5851367 28 COSMIC
COSN18719652 211 COSMIC
COSN2267141 554 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1228018387 1 dbSNP
rs781945909 3 dbSNP
rs375450141 4 dbSNP
rs201483446 6 dbSNP
rs369693449 15 dbSNP
rs373128624 16 dbSNP
rs782809033 17 dbSNP
rs781901876 19 dbSNP
rs370897222 21 dbSNP
rs782703973 24 dbSNP
rs376058939 25 dbSNP
rs369098445 37 dbSNP
rs372941245 38 dbSNP
rs782521887 40 dbSNP
rs1423142863 41 dbSNP
rs1241274561 51 dbSNP
rs782584004 52 dbSNP
rs1461550696 54 dbSNP
rs543529318 64 dbSNP
rs563572711 65 dbSNP
rs1348867954 67 dbSNP
rs770966708 69 dbSNP
rs1359327683 74 dbSNP
rs149902274 80 dbSNP
rs554353553 85 dbSNP
rs890066464 87 dbSNP
rs1383944088 91 dbSNP
rs1380150386 93 dbSNP
rs575885316 93 dbSNP
rs543745973 95 dbSNP
rs558257354 97 dbSNP
rs1386736278 100 dbSNP
rs782532452 101 dbSNP
rs1456915711 107 dbSNP
rs1005741134 113 dbSNP
rs1382858099 114 dbSNP
rs1016593855 116 dbSNP
rs1165348458 119 dbSNP
rs1445187802 125 dbSNP
rs1389292741 127 dbSNP
rs896812869 131 dbSNP
rs994206037 132 dbSNP
rs1024062551 138 dbSNP
rs576805484 139 dbSNP
rs1490189054 144 dbSNP
rs971533141 146 dbSNP
rs979971771 151 dbSNP
rs1248747393 152 dbSNP
rs1360855378 164 dbSNP
rs199507475 166 dbSNP
rs782685091 172 dbSNP
rs990062071 176 dbSNP
rs540745757 177 dbSNP
rs1295762504 180 dbSNP
rs559460569 184 dbSNP
rs1403985359 187 dbSNP
rs1363109634 197 dbSNP
rs1304481871 205 dbSNP
rs945404431 206 dbSNP
rs1369943172 210 dbSNP
rs573859221 211 dbSNP
rs922724901 216 dbSNP
rs1373440684 217 dbSNP
rs934057455 218 dbSNP
rs868912887 221 dbSNP
rs1480247674 223 dbSNP
rs1266837732 227 dbSNP
rs144971753 243 dbSNP
rs911388158 244 dbSNP
rs941652717 245 dbSNP
rs782391401 248 dbSNP
rs561515810 250 dbSNP
rs1341859279 252 dbSNP
rs897362833 254 dbSNP
rs993868680 258 dbSNP
rs1343293796 260 dbSNP
rs531905334 262 dbSNP
rs1284636925 263 dbSNP
rs1405087141 265 dbSNP
rs781950595 279 dbSNP
rs1045780614 282 dbSNP
rs906978181 295 dbSNP
rs1411623052 296 dbSNP
rs1396888137 297 dbSNP
rs1171837744 298 dbSNP
rs1001264450 301 dbSNP
rs542933956 305 dbSNP
rs1201672135 310 dbSNP
rs782231465 315 dbSNP
rs1232403352 323 dbSNP
rs1180222111 326 dbSNP
rs375516448 326 dbSNP
rs957184075 327 dbSNP
rs1440103718 335 dbSNP
rs1274113838 346 dbSNP
rs1203502646 353 dbSNP
rs1011380913 358 dbSNP
rs1320949704 359 dbSNP
rs1264547067 362 dbSNP
rs1020202694 365 dbSNP
rs967675974 366 dbSNP
rs978147055 379 dbSNP
rs373972536 390 dbSNP
rs565114785 391 dbSNP
rs1277291870 392 dbSNP
rs1444272925 399 dbSNP
rs1336319945 406 dbSNP
rs1335835649 409 dbSNP
rs1450258242 409 dbSNP
rs868924920 410 dbSNP
rs868939487 411 dbSNP
rs781938697 414 dbSNP
rs1178802028 417 dbSNP
rs1407321864 417 dbSNP
rs985502636 418 dbSNP
rs1471437445 421 dbSNP
rs1234024321 424 dbSNP
rs911274959 435 dbSNP
rs941536588 436 dbSNP
rs1038480203 445 dbSNP
rs1460204607 446 dbSNP
rs774477530 449 dbSNP
rs1203857707 450 dbSNP
rs918860576 453 dbSNP
rs1281491312 454 dbSNP
rs930205284 455 dbSNP
rs1045423986 458 dbSNP
rs9100 459 dbSNP
rs1314224961 460 dbSNP
rs1243691775 467 dbSNP
rs140869525 476 dbSNP
rs527295406 477 dbSNP
rs906858262 482 dbSNP
rs1448991413 488 dbSNP
rs1316291445 495 dbSNP
rs1381004595 506 dbSNP
rs1402458630 506 dbSNP
rs1163457377 507 dbSNP
rs1443353966 512 dbSNP
rs1387450348 513 dbSNP
rs1184642585 521 dbSNP
rs1240059693 522 dbSNP
rs1217515577 531 dbSNP
rs1447012570 538 dbSNP
rs1290427522 539 dbSNP
rs1220126602 540 dbSNP
rs1361554321 546 dbSNP
rs1315465204 554 dbSNP
rs1213830891 568 dbSNP
rs1359616621 571 dbSNP
rs1268568034 574 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugcaaauuuaaAGUGGGGAAGa 5'
                     || ||||||| 
Target 5' ---------gcUC-CCCCUUCc 3'
1 - 12
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000313269.5 | 3UTR | GCUCCCCCUUCCCCCAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
Click to see details
Click to see details
133 hsa-miR-3179 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT102087 GIGYF1 GRB10 interacting GYF protein 1 2 4
MIRT110061 OGT O-linked N-acetylglucosamine (GlcNAc) transferase 2 6
MIRT112198 BTG2 BTG anti-proliferation factor 2 2 2
MIRT117668 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT146657 MINK1 misshapen like kinase 1 2 2
MIRT175505 ZBTB33 zinc finger and BTB domain containing 33 2 4
MIRT180535 TXNIP thioredoxin interacting protein 2 2
MIRT190624 BCL2L2-PABPN1 BCL2L2-PABPN1 readthrough 2 2
MIRT190650 PABPN1 poly(A) binding protein nuclear 1 2 2
MIRT366902 NONO non-POU domain containing octamer binding 2 2
MIRT443554 ZFP3 ZFP3 zinc finger protein 2 2
MIRT445953 MLLT11 MLLT11, transcription factor 7 cofactor 2 2
MIRT446042 HMCN1 hemicentin 1 2 2
MIRT447968 MSH6 mutS homolog 6 2 2
MIRT448634 ONECUT1 one cut homeobox 1 2 2
MIRT449316 MRO maestro 2 2
MIRT451380 C19orf43 telomerase RNA component interacting RNase 2 2
MIRT451547 CIAPIN1 cytokine induced apoptosis inhibitor 1 2 2
MIRT451807 CDCA3 cell division cycle associated 3 2 4
MIRT451916 ILK integrin linked kinase 2 2
MIRT451938 TMPRSS5 transmembrane protease, serine 5 2 2
MIRT452189 KIAA1456 KIAA1456 2 2
MIRT452498 HMGXB3 HMG-box containing 3 2 2
MIRT452548 ZNF467 zinc finger protein 467 2 2
MIRT453844 SDK1 sidekick cell adhesion molecule 1 2 2
MIRT454515 ZFYVE27 zinc finger FYVE-type containing 27 2 2
MIRT455363 KDM5C lysine demethylase 5C 2 2
MIRT455455 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 2 2
MIRT455628 PABPC1L2B poly(A) binding protein cytoplasmic 1 like 2B 2 10
MIRT455639 PABPC1L2A poly(A) binding protein cytoplasmic 1 like 2A 2 10
MIRT455690 GLO1 glyoxalase I 2 2
MIRT456300 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT456784 MTHFSD methenyltetrahydrofolate synthetase domain containing 2 2
MIRT456819 PIGP phosphatidylinositol glycan anchor biosynthesis class P 2 2
MIRT457566 ZNF34 zinc finger protein 34 2 2
MIRT457604 IDS iduronate 2-sulfatase 2 2
MIRT458236 NXPH3 neurexophilin 3 2 2
MIRT458313 TNFAIP8L3 TNF alpha induced protein 8 like 3 2 2
MIRT458350 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458670 GPR35 G protein-coupled receptor 35 2 2
MIRT459675 VPS37C VPS37C, ESCRT-I subunit 2 2
MIRT461126 RAB36 RAB36, member RAS oncogene family 2 2
MIRT461918 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462301 PPM1H protein phosphatase, Mg2+/Mn2+ dependent 1H 2 2
MIRT463520 ZBTB7B zinc finger and BTB domain containing 7B 2 2
MIRT464378 URM1 ubiquitin related modifier 1 2 2
MIRT464614 UBE4B ubiquitination factor E4B 2 2
MIRT464711 UBE2V1 ubiquitin conjugating enzyme E2 V1 2 2
MIRT465520 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT465974 TMEM189-UBE2V1 TMEM189-UBE2V1 readthrough 2 2
MIRT466058 TMEM189 transmembrane protein 189 2 2
MIRT466548 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT466647 TAGLN2 transgelin 2 2 2
MIRT467357 SP2 Sp2 transcription factor 2 2
MIRT468744 SDC2 syndecan 2 2 2
MIRT470244 PRRC2A proline rich coiled-coil 2A 2 2
MIRT471426 PDIA6 protein disulfide isomerase family A member 6 2 2
MIRT471732 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472190 NHP2L1 small nuclear ribonucleoprotein 13 2 2
MIRT472450 NAV2 neuron navigator 2 2 6
MIRT474563 KLHDC3 kelch domain containing 3 2 2
MIRT474936 KCTD15 potassium channel tetramerization domain containing 15 2 2
MIRT475165 IP6K1 inositol hexakisphosphate kinase 1 2 2
MIRT475399 ICMT isoprenylcysteine carboxyl methyltransferase 2 4
MIRT475426 ICK intestinal cell kinase 2 2
MIRT477090 FAM168A family with sequence similarity 168 member A 2 2
MIRT478458 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT478953 COX15 COX15, cytochrome c oxidase assembly homolog 2 2
MIRT480096 CALR calreticulin 2 2
MIRT481924 ANKRD33B ankyrin repeat domain 33B 2 2
MIRT483217 APOA1 apolipoprotein A1 2 6
MIRT483882 TGIF1 TGFB induced factor homeobox 1 2 2
MIRT483923 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 2 2
MIRT483942 LENG8 leukocyte receptor cluster member 8 2 4
MIRT484209 SUMO1 small ubiquitin-like modifier 1 2 2
MIRT484512 SYT7 synaptotagmin 7 2 2
MIRT484709 RNF11 ring finger protein 11 2 2
MIRT485356 MYO1C myosin IC 2 4
MIRT485615 FOSL1 FOS like 1, AP-1 transcription factor subunit 2 4
MIRT486584 ZNF619 zinc finger protein 619 2 2
MIRT487013 C2orf82 chromosome 2 open reading frame 82 2 2
MIRT487621 C20orf96 chromosome 20 open reading frame 96 2 2
MIRT487801 GPR20 G protein-coupled receptor 20 2 4
MIRT488134 GPR107 G protein-coupled receptor 107 2 2
MIRT488773 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT488854 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT489783 GRINA glutamate ionotropic receptor NMDA type subunit associated protein 1 2 2
MIRT490102 FN3K fructosamine 3 kinase 2 2
MIRT490389 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490434 MYL9 myosin light chain 9 2 2
MIRT490451 GLUD1 glutamate dehydrogenase 1 2 2
MIRT490880 OSBP oxysterol binding protein 2 2
MIRT491037 ALPK3 alpha kinase 3 2 2
MIRT491250 HCN2 hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 2 2
MIRT491748 SEMA3F semaphorin 3F 2 2
MIRT492235 SLC48A1 solute carrier family 48 member 1 2 2
MIRT492490 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT492505 RANBP10 RAN binding protein 10 2 4
MIRT492773 PDGFB platelet derived growth factor subunit B 2 2
MIRT492922 NFAT5 nuclear factor of activated T-cells 5 2 2
MIRT493459 ITFG3 family with sequence similarity 234 member A 2 2
MIRT493654 HDLBP high density lipoprotein binding protein 2 2
MIRT494011 DUSP9 dual specificity phosphatase 9 2 2
MIRT499412 PLCG2 phospholipase C gamma 2 2 4
MIRT499552 C15orf43 telomere repeat binding bouquet formation protein 2 2 2
MIRT501836 NCOA2 nuclear receptor coactivator 2 2 2
MIRT501950 MAT2A methionine adenosyltransferase 2A 2 10
MIRT504066 KCTD12 potassium channel tetramerization domain containing 12 2 4
MIRT504509 PPP1R9B protein phosphatase 1 regulatory subunit 9B 2 2
MIRT508466 HOXB6 homeobox B6 2 4
MIRT512373 CPM carboxypeptidase M 2 2
MIRT513578 EVX1 even-skipped homeobox 1 2 2
MIRT517763 ZNF366 zinc finger protein 366 2 4
MIRT519773 ZNF354B zinc finger protein 354B 2 8
MIRT523568 GGCX gamma-glutamyl carboxylase 2 4
MIRT532802 CLDN11 claudin 11 2 2
MIRT544299 TSPYL1 TSPY like 1 2 2
MIRT544862 MYH2 myosin heavy chain 2 2 4
MIRT556731 KLHL15 kelch like family member 15 2 4
MIRT564347 AKR1B10 aldo-keto reductase family 1 member B10 2 2
MIRT568924 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT569012 CXorf36 chromosome X open reading frame 36 2 2
MIRT569256 FAM129B family with sequence similarity 129 member B 2 2
MIRT569591 PRELP proline and arginine rich end leucine rich repeat protein 2 2
MIRT569779 SAMD14 sterile alpha motif domain containing 14 2 2
MIRT570034 FAM228A family with sequence similarity 228 member A 2 2
MIRT573803 FRMPD4 FERM and PDZ domain containing 4 2 2
MIRT574190 ZNF264 zinc finger protein 264 2 2
MIRT576153 Hmox1 heme oxygenase 1 2 2
MIRT611311 CA8 carbonic anhydrase 8 2 4
MIRT673429 APAF1 apoptotic peptidase activating factor 1 2 2
MIRT674976 SH3BP2 SH3 domain binding protein 2 2 2
MIRT692712 MEAF6 MYST/Esa1 associated factor 6 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3179 Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)
hsa-miR-3179 Osimertinib 71496458 NSC779217 approved sensitive cell line (PC9)
hsa-miR-3179 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-3179 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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