pre-miRNA Information
pre-miRNA hsa-mir-4749   
Genomic Coordinates chr19: 49854591 - 49854651
Description Homo sapiens miR-4749 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4749-3p
Sequence 42| CGCCCCUCCUGCCCCCACAG |61
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN19730808 2 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs147943327 1 dbSNP
rs148982635 2 dbSNP
rs372882504 3 dbSNP
rs200056596 4 dbSNP
rs570340094 5 dbSNP
rs778438436 11 dbSNP
rs748573000 13 dbSNP
rs770230641 14 dbSNP
rs201103722 16 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SNX12   
Synonyms -
Description sorting nexin 12
Transcript NM_013346   
Expression
Putative miRNA Targets on SNX12
3'UTR of SNX12
(miRNA target sites are highlighted)
>SNX12|NM_013346|3'UTR
   1 GAGCCCCTCTCACCACCTGCCCTCTACTTTCCTGCTGAAATGACATTGGTTTTTACACTAAGCCTCTCTCTGTCTTTGAT
  81 CTGAAGTTGGCTGCCCATCTCCTGGCCTGATAGACTGTCTGGCATTGTGCTCCCTGGTACCTGACTACACCATGTGGGCA
 161 CTCTGCTAGGATCCTCTTCTCTGAGGAGAGGTGGGAACCCACAGGCAGATGCCCTTTGCTTGGGGTTGGGGTGGGTGGGT
 241 GGGGGGATTAGACTGGAAGGCAATTTCTTGGGCATTTACCCATGCCAGAAGGCTAACCTGGGGGGAGGGGGGCGCTTGTG
 321 CTGGTGAGGCACTTGGATACATACTGATGCTGCAAGTTCAGGGGATTTTTCTTACTCTTAGGTTTAACCAAGAACACTGA
 401 GCAGGGAAAAACCCTGCCTTTCCTAACTGCATGTATTTTTTCCTTTTTGGAAAGGTGGTAGAGACTCAGAAGCTTTCCTT
 481 GTTTTCTTCAGGCCTGCTCCCAGTTTTCTTAACAGTTTCTTTTGTTGCTTTCTCTCTCCCTTGTTGCTTTCCATGGCAGT
 561 AATCCTCCTAGAGTCCAAGCAGTCTGTTGTATGGAGCAGGGTGTGTGGGTTTTCTGGGCCCATCATTATGGCTGCTTCAG
 641 AGTCAGAAGAAAGCCATAGGGCAGTAGGGGAGCTCCTATTGCCTAGCCCCTCTCCCTTTGTGGCTCCCACTCTAGCTGCC
 721 TATTTTTGCTCATCAGCTGGTGAGTCAGTATGGGCCAGCAGTTCTCCCTCCCTAAGCCCTTGCTACTTTATGGGTTAGCT
 801 TTGCAGGTTTGGTGGCTTGAGGGGTGGGGGCAACTCACCACTGCCAGGTAACTCCCTGAAGGGTGGGAGTGGATTATCTT
 881 CTAGGCTCTTACCCGCGGTAGGGAAGGGCATCAACACTGTCTTCCTTCCATTCTCCTTTCCCCCATCCCATTTAGTGCTG
 961 CCACAGGGCAGAAGCACACAAACCAACCACACAGTCTCTGACTTCTCCTAAGCACTTTGAGTTGTTGAATGGGGCTCAGG
1041 GGCAAGAGTTTTTGCTGCCCTCCCCAGCGTGGTCACAGGGTTATTGAACTGCCTGCACTTGTTTCTCATGCAACTCCAGC
1121 ATTTTCCCCAGAAGTTGAACTATGGATAGCAGCTTGGTATGGATTTCCTAAATCTTAACATTTGAAGCAGCTTCTTGAGG
1201 CTGGCAACTATCCTGGTTTCTGTCTTGGAGGGGGTGGTTTGTTTGCTGGGGCCCAACGTCTGTCCCAAGTGGTGGGGTGA
1281 GAGTAAGTTAACTTTGGTGCCAGGTGAGAGGTGGGGGCTCTTTGCTTAGACTCCCTATCATGGAAAGATTGGAGTTTTCT
1361 ATGCAGGGCACTGTGGAAAAGGATTGCTGATTCTGACTGACCCTGATCAGAGAGATTAGGATTGTATTTTGACATAGGAT
1441 TTGGAACCCATCTAAATGTTGAAGTTCCCTGAGACAGCTCTCCAGCTGCTGAGCCTGCGCCAGGGGCTAAGCAGCCCCTA
1521 ATGAGAGGCTCTGCTCCCTTTCCCACCTCGCCAATGTTGTTGTTGCTGCCTTTTTGATTTGTATCCTCTGTTATAGACAT
1601 TTTTTAAAAACGATTTCCTCTTTCATTGTGCACAAGTGCTGAGAGTCTGAGGCCCCATTTCTGCTGTGTATATATATCCT
1681 GACTCGGGGCTTTTATTCAGCAAACTGTTCATTCTTCTGTCAGACAATGTCATATTCAACTCTGTTCATATTAAACCACT
1761 GTGAAGCAAAAAAAAAAAAAAAAAA
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' gacACCCCCGUCCUCCCCGc 5'
             |||||| | |:||||| 
Target 5' accTGGGGGGA-GGGGGGCg 3'
296 - 314 148.00 -33.00
2
miRNA  3' gacACCCCCGUCCUCCCCGc 5'
             ||| |||  ||||||: 
Target 5' gttTGGTGGCTTGAGGGGTg 3'
807 - 826 145.00 -25.30
3
miRNA  3' gaCACCCCCGUCCUCCCCgc 5'
            ||||| | : |:||||  
Target 5' ggGTGGGTGGGTGGGGGGat 3'
229 - 248 126.00 -24.60
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1170394929 3 dbSNP
rs757092277 5 dbSNP
rs756222868 7 dbSNP
rs1190220471 9 dbSNP
rs1323817572 17 dbSNP
rs1351314641 18 dbSNP
rs1476854016 30 dbSNP
rs375913741 32 dbSNP
rs781081114 40 dbSNP
rs1293346260 47 dbSNP
rs1366347479 56 dbSNP
rs1028613290 71 dbSNP
rs1239601899 72 dbSNP
rs1295991887 73 dbSNP
rs931362077 75 dbSNP
rs1341548902 78 dbSNP
rs1246731422 93 dbSNP
rs777757444 97 dbSNP
rs1292100635 102 dbSNP
rs755580491 104 dbSNP
rs867429326 106 dbSNP
rs1450156855 108 dbSNP
rs995561763 113 dbSNP
rs1245964731 117 dbSNP
rs752197656 122 dbSNP
rs1439374307 130 dbSNP
rs905297788 148 dbSNP
rs1465145544 150 dbSNP
rs767183677 159 dbSNP
rs1388178532 165 dbSNP
rs1448775684 172 dbSNP
rs1163398678 181 dbSNP
rs1415290551 182 dbSNP
rs949436216 188 dbSNP
rs1403291764 191 dbSNP
rs1163571417 202 dbSNP
rs1294530175 219 dbSNP
rs1459747319 220 dbSNP
rs866617262 227 dbSNP
rs1156449614 228 dbSNP
rs754587247 230 dbSNP
rs867452626 232 dbSNP
rs867084306 236 dbSNP
rs1452536266 237 dbSNP
rs1365179842 238 dbSNP
rs751185268 239 dbSNP
rs868097211 240 dbSNP
rs1210272283 241 dbSNP
rs1354311513 243 dbSNP
rs1489339131 244 dbSNP
rs1258669805 247 dbSNP
rs1227987094 278 dbSNP
rs1268961623 282 dbSNP
rs1329614261 283 dbSNP
rs1216181361 284 dbSNP
rs1245955505 285 dbSNP
rs1464416274 290 dbSNP
rs898173608 291 dbSNP
rs73548335 298 dbSNP
rs1232144254 299 dbSNP
rs1331087760 300 dbSNP
rs1412174408 301 dbSNP
rs935485038 302 dbSNP
rs925404188 304 dbSNP
rs893259513 306 dbSNP
rs1388325165 313 dbSNP
rs1003922378 314 dbSNP
rs979604631 321 dbSNP
rs1338811935 337 dbSNP
rs953080419 338 dbSNP
rs1289238332 349 dbSNP
rs1352628830 350 dbSNP
rs1297907913 358 dbSNP
rs532157781 366 dbSNP
rs762154332 370 dbSNP
rs1349618750 372 dbSNP
rs1200995785 375 dbSNP
rs1360720844 396 dbSNP
rs1280562085 413 dbSNP
rs894368438 417 dbSNP
rs759675770 429 dbSNP
rs777072481 444 dbSNP
rs1186297512 452 dbSNP
rs764602436 473 dbSNP
rs1473391932 496 dbSNP
rs1179545073 513 dbSNP
rs753795326 517 dbSNP
rs1478539818 520 dbSNP
rs1199496361 522 dbSNP
rs1400624900 534 dbSNP
rs1414392093 539 dbSNP
rs925323065 552 dbSNP
rs1372457024 557 dbSNP
rs1408254496 574 dbSNP
rs1287917457 583 dbSNP
rs1334951135 596 dbSNP
rs113806567 626 dbSNP
rs1441510816 635 dbSNP
rs978130194 639 dbSNP
rs1434779494 655 dbSNP
rs760692130 657 dbSNP
rs1192622224 672 dbSNP
rs1210035178 690 dbSNP
rs1005168059 691 dbSNP
rs951970561 696 dbSNP
rs1202630476 704 dbSNP
rs1027414367 709 dbSNP
rs1434136230 722 dbSNP
rs1001340396 734 dbSNP
rs1376248306 748 dbSNP
rs41310681 750 dbSNP
rs1169726121 751 dbSNP
rs188271520 758 dbSNP
rs1427823834 767 dbSNP
rs1013582348 774 dbSNP
rs1391798286 804 dbSNP
rs184979378 822 dbSNP
rs774699876 826 dbSNP
rs1329116530 829 dbSNP
rs1233506983 845 dbSNP
rs954261059 846 dbSNP
rs1052451735 852 dbSNP
rs1028979106 856 dbSNP
rs1250258976 862 dbSNP
rs935537172 866 dbSNP
rs770912929 871 dbSNP
rs1211237049 878 dbSNP
rs112274301 894 dbSNP
rs1468285414 895 dbSNP
rs773618485 895 dbSNP
rs181942151 896 dbSNP
rs932162572 904 dbSNP
rs1400957883 917 dbSNP
rs1340795055 924 dbSNP
rs1459685076 933 dbSNP
rs1161631892 950 dbSNP
rs1388349294 960 dbSNP
rs921690029 961 dbSNP
rs1439808912 966 dbSNP
rs962652763 982 dbSNP
rs190486390 993 dbSNP
rs6625757 1008 dbSNP
rs769726926 1010 dbSNP
rs976275470 1010 dbSNP
rs1432811065 1029 dbSNP
rs965826043 1041 dbSNP
rs762128036 1044 dbSNP
rs1172606843 1050 dbSNP
rs1467555025 1054 dbSNP
rs1334623235 1060 dbSNP
rs774012272 1068 dbSNP
rs1250283585 1069 dbSNP
rs1463966822 1071 dbSNP
rs1169761289 1072 dbSNP
rs1186422866 1079 dbSNP
rs1256979732 1081 dbSNP
rs768132384 1086 dbSNP
rs747645703 1096 dbSNP
rs1027549908 1109 dbSNP
rs1024033379 1110 dbSNP
rs1012693026 1111 dbSNP
rs1001307739 1120 dbSNP
rs1265696499 1131 dbSNP
rs1457957220 1133 dbSNP
rs894324019 1135 dbSNP
rs970332330 1143 dbSNP
rs1390530867 1156 dbSNP
rs185528111 1190 dbSNP
rs1288172322 1204 dbSNP
rs1441996658 1207 dbSNP
rs1000118751 1209 dbSNP
rs1309937592 1226 dbSNP
rs1354498867 1230 dbSNP
rs563368678 1236 dbSNP
rs1270472089 1246 dbSNP
rs1014049410 1257 dbSNP
rs896578682 1258 dbSNP
rs1479966415 1261 dbSNP
rs1257952699 1267 dbSNP
rs1052836490 1275 dbSNP
rs367698147 1277 dbSNP
rs1484287219 1295 dbSNP
rs904087204 1302 dbSNP
rs945397192 1320 dbSNP
rs1256898045 1330 dbSNP
rs1473067046 1333 dbSNP
rs1184548930 1340 dbSNP
rs1413940780 1343 dbSNP
rs1044032058 1348 dbSNP
rs1158306235 1352 dbSNP
rs748832226 1362 dbSNP
rs754463885 1365 dbSNP
rs779422490 1372 dbSNP
rs6780 1374 dbSNP
rs1410078678 1394 dbSNP
rs1040553738 1402 dbSNP
rs779677144 1412 dbSNP
rs1334294092 1413 dbSNP
rs1349023185 1432 dbSNP
rs745777147 1432 dbSNP
rs1302400491 1443 dbSNP
rs781171041 1448 dbSNP
rs1231674743 1463 dbSNP
rs1279772088 1466 dbSNP
rs1398102132 1467 dbSNP
rs757566990 1495 dbSNP
rs1051209422 1496 dbSNP
rs932790212 1498 dbSNP
rs1466014785 1499 dbSNP
rs193203361 1500 dbSNP
rs1480421318 1512 dbSNP
rs921444862 1515 dbSNP
rs907633676 1522 dbSNP
rs1434886187 1538 dbSNP
rs1425519708 1549 dbSNP
rs1161189168 1550 dbSNP
rs1171627835 1552 dbSNP
rs983059641 1554 dbSNP
rs1429755908 1563 dbSNP
rs1309490376 1566 dbSNP
rs930338666 1566 dbSNP
rs920501720 1576 dbSNP
rs1472609540 1586 dbSNP
rs189909091 1594 dbSNP
rs1352462037 1606 dbSNP
rs769467268 1611 dbSNP
rs184299094 1612 dbSNP
rs757147365 1620 dbSNP
rs908840125 1631 dbSNP
rs1218008314 1642 dbSNP
rs141364352 1654 dbSNP
rs982396093 1664 dbSNP
rs1456488520 1672 dbSNP
rs751344181 1685 dbSNP
rs1307174295 1686 dbSNP
rs11549129 1689 dbSNP
rs11549130 1694 dbSNP
rs11134 1697 dbSNP
rs1209587990 1703 dbSNP
rs1191674303 1708 dbSNP
rs1012684407 1715 dbSNP
rs1355272320 1727 dbSNP
rs1449993858 1727 dbSNP
rs754008523 1732 dbSNP
rs1170016535 1734 dbSNP
rs1284413254 1735 dbSNP
rs1246439115 1744 dbSNP
rs1416738804 1746 dbSNP
rs1374018460 1769 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_ControlB_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control B
Location of target site ENST00000374274.3 | 3UTR | GCAAGAGUUUUUGCUGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
63 hsa-miR-4749-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT082256 MED29 mediator complex subunit 29 2 4
MIRT112161 OTUD3 OTU deubiquitinase 3 2 2
MIRT150036 MIDN midnolin 2 2
MIRT246308 HIST2H2AA3 histone cluster 2 H2A family member a3 2 4
MIRT246320 HIST2H2AA4 histone cluster 2 H2A family member a4 2 4
MIRT248254 SP1 Sp1 transcription factor 2 2
MIRT257944 GIGYF1 GRB10 interacting GYF protein 1 2 2
MIRT466973 STARD7 StAR related lipid transfer domain containing 7 2 4
MIRT492322 SETD1B SET domain containing 1B 2 2
MIRT496204 EFCAB1 EF-hand calcium binding domain 1 2 2
MIRT497568 CCR6 C-C motif chemokine receptor 6 2 2
MIRT502990 CCDC71L coiled-coil domain containing 71 like 2 8
MIRT508300 SIX5 SIX homeobox 5 2 4
MIRT522472 ZAK mitogen-activated protein kinase kinase kinase 20 2 2
MIRT525825 VIMP selenoprotein S 2 4
MIRT528154 BCL2L1 BCL2 like 1 2 2
MIRT532606 SPTLC2 serine palmitoyltransferase long chain base subunit 2 2 2
MIRT551302 RPRM reprimo, TP53 dependent G2 arrest mediator homolog 2 2
MIRT568777 FAM53C family with sequence similarity 53 member C 2 6
MIRT570896 METTL21A methyltransferase like 21A 2 2
MIRT570963 TMBIM4 transmembrane BAX inhibitor motif containing 4 2 2
MIRT571167 ZNF85 zinc finger protein 85 2 2
MIRT576751 Tmem127 transmembrane protein 127 2 2
MIRT609854 DAZAP2 DAZ associated protein 2 2 2
MIRT627101 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT637060 PRKAG1 protein kinase AMP-activated non-catalytic subunit gamma 1 2 2
MIRT639423 PKP1 plakophilin 1 2 2
MIRT643208 TYW3 tRNA-yW synthesizing protein 3 homolog 2 4
MIRT646251 PRSS38 protease, serine 38 2 2
MIRT647145 CYP27C1 cytochrome P450 family 27 subfamily C member 1 2 2
MIRT647429 ZKSCAN2 zinc finger with KRAB and SCAN domains 2 2 2
MIRT650666 GAPDHP44 glyceraldehyde 3 phosphate dehydrogenase pseudogene 44 2 2
MIRT651816 USP49 ubiquitin specific peptidase 49 2 2
MIRT657376 HMGA1 high mobility group AT-hook 1 2 2
MIRT658105 FOXK1 forkhead box K1 2 2
MIRT658161 FCHSD1 FCH and double SH3 domains 1 2 2
MIRT662754 LRRC3C leucine rich repeat containing 3C 2 2
MIRT667209 NIPAL1 NIPA like domain containing 1 2 2
MIRT687003 RPL35 ribosomal protein L35 2 2
MIRT707057 NACC2 NACC family member 2 2 2
MIRT709048 MRO maestro 2 2
MIRT709054 MGAT5B mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B 2 2
MIRT709446 VWA2 von Willebrand factor A domain containing 2 2 2
MIRT709847 SNX12 sorting nexin 12 2 2
MIRT710790 IFNLR1 interferon lambda receptor 1 2 2
MIRT711696 GMPR guanosine monophosphate reductase 2 2
MIRT712462 KCNC3 potassium voltage-gated channel subfamily C member 3 2 2
MIRT713884 MOB3A MOB kinase activator 3A 2 2
MIRT715329 NTN1 netrin 1 2 2
MIRT715927 CHD4 chromodomain helicase DNA binding protein 4 2 2
MIRT716533 ATF5 activating transcription factor 5 2 2
MIRT716937 CACNB1 calcium voltage-gated channel auxiliary subunit beta 1 2 2
MIRT717007 MFSD6 major facilitator superfamily domain containing 6 2 2
MIRT719139 DPYSL5 dihydropyrimidinase like 5 2 2
MIRT720853 MEF2D myocyte enhancer factor 2D 2 2
MIRT721484 LTB4R2 leukotriene B4 receptor 2 2 2
MIRT721517 DKK3 dickkopf WNT signaling pathway inhibitor 3 2 2
MIRT722895 LRRC20 leucine rich repeat containing 20 2 2
MIRT723066 GGA1 golgi associated, gamma adaptin ear containing, ARF binding protein 1 2 2
MIRT723086 INSIG1 insulin induced gene 1 2 2
MIRT723353 ASCL2 achaete-scute family bHLH transcription factor 2 2 2
MIRT723483 MINOS1 mitochondrial inner membrane organizing system 1 2 2
MIRT724576 NOTCH2 notch 2 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4749 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4749 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4749 Paclitaxel 36314 NSC125973 approved resistant cell line (W1)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant High Hypopharyngeal Cancer cell line (FaDu)
hsa-miR-4749-3p Tamoxifen+Fulvestrant sensitive cell line (LCC9)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-4749-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved resistant cell line (OVSAHO)
hsa-miR-4749-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (TOV-112D)

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