miRTarBase - #MIRT557394


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pre-miRNA Information
pre-miRNA hsa-mir-938   
Genomic Coordinates chr10: 29602264 - 29602346
Synonyms MIRN938, hsa-mir-938, MIR938
Description Homo sapiens miR-938 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-938
Sequence 15| UGCCCUUAAAGGUGAACCCAGU |36
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN28704008 2 COSMIC
COSN31533921 5 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs12416605 2 dbSNP
rs1348880424 3 dbSNP
rs1205636191 4 dbSNP
rs757919276 12 dbSNP
rs754296125 14 dbSNP
rs573596343 17 dbSNP
rs756660742 18 dbSNP
rs753092730 21 dbSNP
Putative Targets

Gene Information
Gene Symbol H3F3C   
Synonyms H3.5
Description H3 histone family member 3C
Transcript NM_001013699   
Expression
Putative miRNA Targets on H3F3C
3'UTR of H3F3C
(miRNA target sites are highlighted)		 
>H3F3C|NM_001013699|3'UTR
   1 GTGAAGGCAGTTTTTATGGCATTTTGTAGTAAATTCTGTAAAATACTTTGGTTTAATTGGTGACTTTTTTTGTAAGAAAT
  81 TGTTTATATGTTGCATTTGTACTTAAGTCATTCCATCTTTCACTCAGGATGAATGCGAAAAGTGACTGTTTACAGACCTC
 161 AGTGATGTCAGCACTGTTGCTCAGGAGTGACAAGTTGTTAATATGCAAAACGGATGCGTGATATTTCTTGCTTCTCATGA
 241 TGCATGTTTCTGTATGTTAATGACTTGTTGGGTAGCTATTAAGGTACTAGAATTGATAAATGTGTACAACAGGGTCCTTT
 321 TGCAATAAAACTGGTTATGACTTGATCCAAGTGTTTAACAATTGGGGCTGTTAAGTCTGACCATACATCACTGTGATAGA
 401 ATGTAGGCTTTTTCAAGGGTGAAGATACAAACCTTAACCACAGTGTAACTTATAGTTTCCTTTAAAAAAAAAAAATTAAA
 481 CCTGGCAGCTATAGAATACAATATGTGCATTTATAATAGCTATTTTATATATTGTAGTGTCAACATTTTCAAATTAAATG
 561 TTTTACATTCACAAAAAAAAAAAAAAAA
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' ugACCCAAGUGGA-AAUUCCcgu 5'
            |||||  | || ||||||   
Target 5' gtTGGGT--AGCTATTAAGGtac 3'
 267 - 287 124.00 -13.90
2 
miRNA  3' ugaCCCAAGUGGAAAUUCCCGu 5'
             | |||:| |  | :|||| 
Target 5' caaGTGTTTAACAATTGGGGCt 3'
 348 - 369 111.00 -9.40
3 
miRNA  3' ugACCCAAGUGGAAAUUCCCGu 5'
            | ||  | ::|| |||||: 
Target 5' tgTAGG--CTTTTTCAAGGGTg 3'
 402 - 421 108.00 -8.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28569386 21 COSMIC
COSN31496939 29 COSMIC
COSN30181184 35 COSMIC
COSN31605062 36 COSMIC
COSN28564161 59 COSMIC
COSN31612228 80 COSMIC
COSN31503891 87 COSMIC
COSN22985862 93 COSMIC
COSN30496501 108 COSMIC
COSN30476199 113 COSMIC
COSN25444405 157 COSMIC
COSN26676132 169 COSMIC
COSN26482337 191 COSMIC
COSN31530200 206 COSMIC
COSN31605744 211 COSMIC
COSN7366436 270 COSMIC
COSN31529639 290 COSMIC
COSN31486964 295 COSMIC
COSN16790670 312 COSMIC
COSN8585998 322 COSMIC
COSN26576320 463 COSMIC
COSN20109437 464 COSMIC
COSN16997395 555 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs761499258 1 dbSNP
rs3759294 2 dbSNP
rs142715943 6 dbSNP
rs780015655 7 dbSNP
rs1250242225 10 dbSNP
rs1179540799 14 dbSNP
rs767732062 16 dbSNP
rs769657421 16 dbSNP
rs745852050 17 dbSNP
rs377269815 18 dbSNP
rs757060937 21 dbSNP
rs1357058467 26 dbSNP
rs752854284 27 dbSNP
rs907228430 28 dbSNP
rs1314965080 31 dbSNP
rs779174204 33 dbSNP
rs368275926 34 dbSNP
rs753916059 35 dbSNP
rs372895813 36 dbSNP
rs879060802 39 dbSNP
rs1385740266 42 dbSNP
rs368780178 45 dbSNP
rs1295862763 46 dbSNP
rs761036951 47 dbSNP
rs1363686285 49 dbSNP
rs757527161 57 dbSNP
rs1374213354 59 dbSNP
rs540646834 60 dbSNP
rs1445008763 61 dbSNP
rs1322930052 65 dbSNP
rs541802300 71 dbSNP
rs143556916 72 dbSNP
rs764249459 76 dbSNP
rs1264223409 93 dbSNP
rs1358481481 97 dbSNP
rs1054679612 107 dbSNP
rs572761501 114 dbSNP
rs138634363 117 dbSNP
rs1456664547 121 dbSNP
rs11051596 126 dbSNP
rs974533256 130 dbSNP
rs752461643 131 dbSNP
rs911586361 132 dbSNP
rs1370122573 133 dbSNP
rs1385901900 136 dbSNP
rs1169411754 151 dbSNP
rs765426567 153 dbSNP
rs983077934 158 dbSNP
rs373516851 160 dbSNP
rs950671627 184 dbSNP
rs578257793 185 dbSNP
rs1027538541 194 dbSNP
rs994687534 195 dbSNP
rs1391827358 205 dbSNP
rs1257554849 211 dbSNP
rs1316270451 212 dbSNP
rs1193629804 216 dbSNP
rs112907660 217 dbSNP
rs11051595 218 dbSNP
rs1001648883 221 dbSNP
rs765812183 222 dbSNP
rs907277126 225 dbSNP
rs1490376754 232 dbSNP
rs1192263810 237 dbSNP
rs1045763627 238 dbSNP
rs1222449541 241 dbSNP
rs1381002032 246 dbSNP
rs142261223 262 dbSNP
rs774128699 265 dbSNP
rs1272344452 275 dbSNP
rs1228627603 277 dbSNP
rs549218527 290 dbSNP
rs1404946994 310 dbSNP
rs770770505 310 dbSNP
rs1383671847 312 dbSNP
rs1326143493 333 dbSNP
rs1338472478 339 dbSNP
rs1220549672 348 dbSNP
rs1279009072 349 dbSNP
rs1054731197 356 dbSNP
rs1230787697 357 dbSNP
rs36058687 361 dbSNP
rs1215739444 362 dbSNP
rs1483521795 362 dbSNP
rs573769421 364 dbSNP
rs1388697027 366 dbSNP
rs566775619 368 dbSNP
rs189860374 372 dbSNP
rs1193828666 375 dbSNP
rs1424028040 388 dbSNP
rs1366330050 407 dbSNP
rs1039594749 408 dbSNP
rs1379684719 424 dbSNP
rs1435763535 426 dbSNP
rs1302597251 430 dbSNP
rs533042890 433 dbSNP
rs1298055061 448 dbSNP
rs1359203057 464 dbSNP
rs944512888 464 dbSNP
rs1289586713 476 dbSNP
rs1303701552 476 dbSNP
rs34845138 476 dbSNP
rs397851048 476 dbSNP
rs398076550 476 dbSNP
rs564070029 476 dbSNP
rs1312510779 481 dbSNP
rs1372318198 493 dbSNP
rs878931549 497 dbSNP
rs772853625 502 dbSNP
rs1355854605 503 dbSNP
rs1216668936 511 dbSNP
rs1245678268 518 dbSNP
rs550362047 523 dbSNP
rs867509832 527 dbSNP
rs1192531273 528 dbSNP
rs1267619641 529 dbSNP
rs1454937179 537 dbSNP
rs950403798 539 dbSNP
rs1371079943 543 dbSNP
rs920230531 544 dbSNP
rs973321439 546 dbSNP
rs959531675 566 dbSNP
rs1349320386 569 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 440093.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ugACCC----AAGUGGAAAUUCCCGu 5'
            ||||    ||:|::| ||||||| 
Target 5' acUGGGGGAUUUUAUUUAUAAGGGCu 3'
 		6 - 31
2 
miRNA  3' ugacccaaGUGGAAAUUcccgu 5'
                  |||   |||     
Target 5' --------CAC---UAAcuggg 3'
 		1 - 11
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000340398.3 | 3UTR | CACUAACUGGGGGAUUUUAUUUAUAAGGGCUCUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
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
GSE38226 Liver fibrosis -0.476 1.5e-2 -0.324 7.6e-2 21 Click to see details
GSE28260 Renal cortex and medulla -0.578 1.9e-2 -0.549 2.6e-2 13 Click to see details
GSE28544 Breast cancer 0.275 9.7e-2 0.318 6.5e-2 24 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.105 3.1e-1 -0.107 3.1e-1 25 Click to see details
GSE26953 Aortic valvular endothelial cells 0.106 3.1e-1 -0.012 4.8e-1 24 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.08 3.7e-1 -0.653 9.0e-4 20 Click to see details
GSE42095 Differentiated embryonic stem cells -0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
GSE42095 Differentiated embryonic stem cells -0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
-0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
-0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
-0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
-0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
-0.005 4.9e-1 -0.026 4.5e-1 23 Click to see details
54 hsa-miR-938 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT073757 NUBP1 nucleotide binding protein 1 2 2
MIRT092006 SNRK SNF related kinase 2 12
MIRT218174 MRPL18 mitochondrial ribosomal protein L18 2 2
MIRT485452 IVNS1ABP influenza virus NS1A binding protein 2 2
MIRT489857 ATP2A3 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 2 2
MIRT495407 SPPL3 signal peptide peptidase like 3 2 4
MIRT495762 ZNF607 zinc finger protein 607 2 2
MIRT497391 RALY RALY heterogeneous nuclear ribonucleoprotein 2 2
MIRT499227 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT507059 H3F3B H3 histone family member 3B 2 2
MIRT513671 SOCS5 suppressor of cytokine signaling 5 2 8
MIRT526922 IRGQ immunity related GTPase Q 2 4
MIRT527488 OCIAD1 OCIA domain containing 1 2 2
MIRT527566 ADCY7 adenylate cyclase 7 2 2
MIRT528081 NOL9 nucleolar protein 9 2 2
MIRT528535 CYP2C19 cytochrome P450 family 2 subfamily C member 19 2 4
MIRT533896 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT536523 KCTD10 potassium channel tetramerization domain containing 10 2 2
MIRT541382 CDKN1A cyclin dependent kinase inhibitor 1A 2 2
MIRT550254 FAM120AOS family with sequence similarity 120A opposite strand 2 2
MIRT555975 NPTN neuroplastin 2 2
MIRT557394 H3F3C H3 histone family member 3C 2 2
MIRT568594 ADM adrenomedullin 2 2
MIRT571876 NCL nucleolin 2 2
MIRT572443 TRIM10 tripartite motif containing 10 2 2
MIRT610589 PRDM1 PR/SET domain 1 2 2
MIRT614044 THBS2 thrombospondin 2 2 2
MIRT618412 ATP2A2 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 2 2
MIRT623398 LHFPL2 LHFPL tetraspan subfamily member 2 2 2
MIRT623948 FBXO47 F-box protein 47 2 2
MIRT625349 MGLL monoglyceride lipase 2 2
MIRT635447 FAM180B family with sequence similarity 180 member B 2 2
MIRT638249 SLC16A9 solute carrier family 16 member 9 2 2
MIRT642662 RGS6 regulator of G protein signaling 6 2 2
MIRT646431 ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 2 2
MIRT647172 ARGFX arginine-fifty homeobox 2 2
MIRT654891 POU2F1 POU class 2 homeobox 1 2 2
MIRT659337 CSE1L chromosome segregation 1 like 2 2
MIRT667407 MGAT5 mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase 2 2
MIRT698892 SPTBN2 spectrin beta, non-erythrocytic 2 2 2
MIRT703841 ETV3 ETS variant 3 2 2
MIRT708322 NT5C 5', 3'-nucleotidase, cytosolic 2 2
MIRT708934 CRY2 cryptochrome circadian clock 2 2 2
MIRT709745 UBD ubiquitin D 2 2
MIRT710265 FAM107A family with sequence similarity 107 member A 2 2
MIRT712576 ATP2B4 ATPase plasma membrane Ca2+ transporting 4 2 2
MIRT712645 TXNL4A thioredoxin like 4A 2 2
MIRT714833 SCAMP2 secretory carrier membrane protein 2 2 2
MIRT720673 SLC39A13 solute carrier family 39 member 13 2 2
MIRT723041 MAPT microtubule associated protein tau 2 2
MIRT723669 CTC1 CST telomere replication complex component 1 2 2
MIRT723772 ROBO4 roundabout guidance receptor 4 2 2
MIRT723812 OR1L8 olfactory receptor family 1 subfamily L member 8 2 2
MIRT736795 RBM5 RNA binding motif protein 5 2 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-938 Emodin NULL 3220 Microarray K562 cells 23744534 2013 down-regualted
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-938 Paclitaxel 36314 NSC125973 approved sensitive High Non-Small Cell Lung Cancer cell line (H358, H1155)
hsa-miR-938 Vemurafenib 42611257 NSC761431 approved resistant cell line (LM16)
hsa-miR-938 Vemurafenib 42611257 NSC761431 approved resistant cell line (LM43)
hsa-miR-938 4-Hydroxytamoxifen+Tamoxifen sensitive cell line (LY2)
hsa-miR-938 Ethanol+Tamoxifen sensitive cell line (LY2)
hsa-miR-938 Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-938 Oxaliplatin 6857599 NSC266046 approved sensitive cell line (IGROV-1)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (IGROV-1)
hsa-miR-938 Paclitaxel 36314 NSC125973 approved sensitive cell line (PC3PR70)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-938 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-938 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)

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