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 GGA1   
Synonyms -
Description golgi associated, gamma adaptin ear containing, ARF binding protein 1
Transcript NM_001001560   
Other Transcripts NM_001172687 , NM_001172688 , NM_013365   
Expression
Putative miRNA Targets on GGA1
3'UTR of GGA1
(miRNA target sites are highlighted)
>GGA1|NM_001001560|3'UTR
   1 AACAGAGGGGCTGGGGAGAGGAAGGGGCAGAGGGACCGGTCACTGTCCAGCCTGGAGGGAGGCATTGGTGGCCAAGGACA
  81 CCCTTTGTTGCCCATGGCCATTCACCCCCAGGCCTGGTGCTTCTCCCCACACCCCTGTAGGCCTCAAGTGACTCTTCCCC
 161 CTCCTGCTCCGGCCCCGCCCCTGCTGAGCCAAACCCAGTAGGAGGCTGGGCCTGGGTTTGTGCCGCTGGGGTCTCCATCA
 241 CCGGGACCTGGAGAGGGAGGGGCTGTGTAGCCTTGGAAGAACTTGGGTCATGGGGAGGAAGCACAGCTGTTGGGGAAGGG
 321 CCAGGACCTCAGGCCCAGCCCCAACCCCAGCTGGGGTGGGGTCTTCCCCACCTGTCTCTTATGCCTTATGGGAAGGCCCA
 401 GCCATAACTCGGGGGCCATGCTGGAGCTGGGGACCAGCTTAGGCCTCCTCCATAGGAACCCAGTGACTGGGGGGTGACGC
 481 CTACACCCCCAGCTATTTGCACTCTGGTGTGTGGTTTGACTCTGCTTTTCTTCCGGATTGGCCCTGTGGTCACAGCCTCA
 561 GGGGGCCAGGCTGGGGGAACCTCACCTGGCCCGTACTCCTGGGGGTTTCCCTTTGCCATTGGGCCCCCTGAGGGACTGTG
 641 GGGGCTCAAGGGTAATGCCAGAGGCCCATGGCCCCAGCGAGGGGCTGTGGGGCACCTAGAGTTCTCGGTGTGTCTCCTTC
 721 ATTCATTGGCCTCTGCTGGGGCCTCCTATGGGTGTCTTACGTCTGTCCATCCATCTGTCCGTGGTCAGAAGTGGGGTCAG
 801 TGTGTGAGTGAGAGCAGGAGTATTTATGAAAATAAAACGTCGTTTTTCCTGGAAAAAAAAAAAAAAAAAAAAAAAAAA
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' gacctGGAGAGGGAGGGGCt 3'
245 - 264 155.00 -19.40
2
miRNA  3' gacACCCCCGUC-CUCCCCGc 5'
             |||   ||| ||||||| 
Target 5' ccaTGGCCCCAGCGAGGGGCt 3'
666 - 686 153.00 -19.00
3
miRNA  3' gacacccccGUCCUCCCCGc 5'
                   || ||||||| 
Target 5' -------aaCA-GAGGGGCt 3'
1 - 12 142.00 -13.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31504436 4 COSMIC
COSN30176709 93 COSMIC
COSN30139558 128 COSMIC
COSN32064989 258 COSMIC
COSN1261718 334 COSMIC
COSN23823581 360 COSMIC
COSN20701826 397 COSMIC
COSN4624302 574 COSMIC
COSN25035771 765 COSMIC
COSN19513479 782 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs764981703 6 dbSNP
rs1484807869 8 dbSNP
rs532984852 9 dbSNP
rs1009534870 10 dbSNP
rs1484207503 13 dbSNP
rs755556783 15 dbSNP
rs551685246 17 dbSNP
rs1050519302 19 dbSNP
rs570004716 21 dbSNP
rs758873690 24 dbSNP
rs376994676 28 dbSNP
rs1440850991 29 dbSNP
rs1161998834 30 dbSNP
rs1343793206 35 dbSNP
rs1453555656 38 dbSNP
rs747311915 39 dbSNP
rs771051099 44 dbSNP
rs1450477069 46 dbSNP
rs1336173332 53 dbSNP
rs1008616943 59 dbSNP
rs530720099 60 dbSNP
rs777430945 62 dbSNP
rs900788421 66 dbSNP
rs558289893 68 dbSNP
rs11913935 73 dbSNP
rs1033006857 76 dbSNP
rs1285650428 78 dbSNP
rs184023198 80 dbSNP
rs1219489657 82 dbSNP
rs1277232000 104 dbSNP
rs1309946691 105 dbSNP
rs1022541258 106 dbSNP
rs968706962 108 dbSNP
rs941752491 125 dbSNP
rs1010323606 126 dbSNP
rs1418931155 133 dbSNP
rs1021170827 140 dbSNP
rs878883509 142 dbSNP
rs1179634823 153 dbSNP
rs1475886652 155 dbSNP
rs1257645062 156 dbSNP
rs1210016060 157 dbSNP
rs534279990 157 dbSNP
rs748909656 158 dbSNP
rs917074641 161 dbSNP
rs535132779 162 dbSNP
rs1356124927 164 dbSNP
rs1292772232 165 dbSNP
rs1006540283 170 dbSNP
rs187632759 172 dbSNP
rs1290031690 176 dbSNP
rs1423084665 177 dbSNP
rs191111308 178 dbSNP
rs538690480 180 dbSNP
rs1462715675 181 dbSNP
rs1417884476 183 dbSNP
rs1186606226 188 dbSNP
rs920263881 196 dbSNP
rs1263742574 199 dbSNP
rs944443254 200 dbSNP
rs557230327 209 dbSNP
rs1215735066 211 dbSNP
rs11913963 225 dbSNP
rs771616905 226 dbSNP
rs1328330321 241 dbSNP
rs908013031 243 dbSNP
rs892629976 244 dbSNP
rs542814406 246 dbSNP
rs1436677104 247 dbSNP
rs542109262 250 dbSNP
rs944876258 260 dbSNP
rs1273885838 277 dbSNP
rs1394753219 279 dbSNP
rs1044290022 280 dbSNP
rs1040549859 284 dbSNP
rs776052429 292 dbSNP
rs1215795143 295 dbSNP
rs1374335602 298 dbSNP
rs1002886760 309 dbSNP
rs372261360 310 dbSNP
rs896516333 315 dbSNP
rs1013668667 324 dbSNP
rs1015726840 333 dbSNP
rs1054344810 335 dbSNP
rs1252589778 342 dbSNP
rs1341328225 344 dbSNP
rs764463061 346 dbSNP
rs1341516105 348 dbSNP
rs573628396 352 dbSNP
rs541098984 357 dbSNP
rs1293613821 363 dbSNP
rs1251991193 366 dbSNP
rs1227270337 370 dbSNP
rs1340671867 371 dbSNP
rs893144191 375 dbSNP
rs776882522 376 dbSNP
rs1245201876 379 dbSNP
rs559524141 383 dbSNP
rs1476546469 386 dbSNP
rs532947833 390 dbSNP
rs574722460 396 dbSNP
rs564331586 397 dbSNP
rs1324765478 398 dbSNP
rs561619827 402 dbSNP
rs1189273271 405 dbSNP
rs1397948175 409 dbSNP
rs1298264026 411 dbSNP
rs971859187 412 dbSNP
rs1175494976 420 dbSNP
rs2269547 424 dbSNP
rs1166030297 430 dbSNP
rs951976457 435 dbSNP
rs1196967964 441 dbSNP
rs1405136246 444 dbSNP
rs765526293 445 dbSNP
rs1251257853 446 dbSNP
rs1003363249 447 dbSNP
rs1195293885 449 dbSNP
rs1347733542 453 dbSNP
rs1482146487 462 dbSNP
rs1034893001 469 dbSNP
rs1436880343 469 dbSNP
rs944412287 469 dbSNP
rs369683055 470 dbSNP
rs1297640087 472 dbSNP
rs913618462 475 dbSNP
rs78147582 479 dbSNP
rs990745773 480 dbSNP
rs1226010970 484 dbSNP
rs1435285797 487 dbSNP
rs184078390 496 dbSNP
rs1357051053 503 dbSNP
rs574581379 506 dbSNP
rs188413658 512 dbSNP
rs1364590295 521 dbSNP
rs983546469 529 dbSNP
rs907605667 534 dbSNP
rs944487001 535 dbSNP
rs557491415 536 dbSNP
rs547218473 550 dbSNP
rs932201451 555 dbSNP
rs897216899 557 dbSNP
rs1207247649 558 dbSNP
rs543293346 560 dbSNP
rs1351911626 561 dbSNP
rs1054646500 565 dbSNP
rs547064471 572 dbSNP
rs996016171 574 dbSNP
rs7582 578 dbSNP
rs952002140 578 dbSNP
rs1294609021 587 dbSNP
rs946049012 593 dbSNP
rs752616902 594 dbSNP
rs1185566632 595 dbSNP
rs756015817 597 dbSNP
rs1402214998 600 dbSNP
rs1369534411 604 dbSNP
rs965940731 605 dbSNP
rs1455865283 614 dbSNP
rs913587584 619 dbSNP
rs966413883 620 dbSNP
rs979620391 624 dbSNP
rs907283970 625 dbSNP
rs1410658532 629 dbSNP
rs1489772214 629 dbSNP
rs191618621 631 dbSNP
rs1207644699 643 dbSNP
rs1326644401 644 dbSNP
rs550573196 645 dbSNP
rs1233344437 650 dbSNP
rs1355103127 651 dbSNP
rs1320828196 652 dbSNP
rs894995296 659 dbSNP
rs11543987 661 dbSNP
rs1432260050 663 dbSNP
rs1326759393 668 dbSNP
rs1319661397 672 dbSNP
rs11543986 673 dbSNP
rs1340972682 679 dbSNP
rs1244029440 683 dbSNP
rs1404807185 685 dbSNP
rs1411758397 690 dbSNP
rs778616581 705 dbSNP
rs918141485 708 dbSNP
rs949631620 709 dbSNP
rs757083128 711 dbSNP
rs1037012489 713 dbSNP
rs1254471579 716 dbSNP
rs1213978444 718 dbSNP
rs952084738 729 dbSNP
rs1330979592 732 dbSNP
rs1320553988 735 dbSNP
rs1287162808 737 dbSNP
rs983131268 738 dbSNP
rs1229168839 744 dbSNP
rs1339999220 749 dbSNP
rs1296873794 751 dbSNP
rs1225884996 753 dbSNP
rs897185789 755 dbSNP
rs1267734254 759 dbSNP
rs778513478 761 dbSNP
rs965727653 762 dbSNP
rs745577323 764 dbSNP
rs1390084117 773 dbSNP
rs1167314024 777 dbSNP
rs549571871 780 dbSNP
rs185287549 781 dbSNP
rs11912295 782 dbSNP
rs1186076101 785 dbSNP
rs747501770 788 dbSNP
rs1244408875 791 dbSNP
rs1206004207 796 dbSNP
rs534167842 810 dbSNP
rs1273800288 811 dbSNP
rs747955533 816 dbSNP
rs1158979884 819 dbSNP
rs1349721683 820 dbSNP
rs1410752719 821 dbSNP
rs1303891555 826 dbSNP
rs1017402676 828 dbSNP
rs965909633 830 dbSNP
rs1455365343 839 dbSNP
rs553099672 840 dbSNP
rs1020563204 842 dbSNP
rs577814875 843 dbSNP
rs1041682157 849 dbSNP
rs1376387365 852 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_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + A ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gacacccccgucCUCCCCGc 5'
                      ||||||| 
Target 5' -----------aGAGGGGCu 3'
1 - 9
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 GSM4903828
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID21_9124
Location of target site NM_001001560 | 3UTR | AGGAGGCUGGGCCUGGGUUUGUGCCGCUGGGGUCUCCAUCACCGGGACCUGGAGAGGGAGGGGCUGUGUAGCCUUGGAAGAACUUGGGUCAUGGGGAGGAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset Chi_124A_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell miR-124 + A
Location of target site ENST00000343632.4 | 3UTR | AGAGGGGCUGGGGAGAGGAAG
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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