miRTarBase - #MIRT468196


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pre-miRNA Information
pre-miRNA hsa-mir-4641   
Genomic Coordinates chr6: 41598723 - 41598788
Description Homo sapiens miR-4641 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4641
Sequence 42| UGCCCAUGCCAUACUUUUGCCUCA |65
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN26639373 2 COSMIC
COSN26565394 8 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1373321216 2 dbSNP
rs1308336996 3 dbSNP
rs77674981 8 dbSNP
rs1207697996 10 dbSNP
rs764486175 13 dbSNP
rs751699264 14 dbSNP
rs1264377902 18 dbSNP
rs1359658375 21 dbSNP
rs757278893 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SGK1   
Synonyms SGK
Description serum/glucocorticoid regulated kinase 1
Transcript NM_001143676   
Other Transcripts NM_001143677 , NM_001143678 , NM_005627   
Expression
Putative miRNA Targets on SGK1
3'UTR of SGK1
(miRNA target sites are highlighted)		 
>SGK1|NM_001143676|3'UTR
   1 ACCCTGTTAGGGCTTGGTTTTAAAGGATTTTATGTGTGTTTCCGAATGTTTTAGTTAGCCTTTTGGTGGAGCCGCCAGCT
  81 GACAGGACATCTTACAAGAGAATTTGCACATCTCTGGAAGCTTAGCAATCTTATTGCACACTGTTCGCTGGAAGCTTTTT
 161 GAAGAGCACATTCTCCTCAGTGAGCTCATGAGGTTTTCATTTTTATTCTTCCTTCCAACGTGGTGCTATCTCTGAAACGA
 241 GCGTTAGAGTGCCGCCTTAGACGGAGGCAGGAGTTTCGTTAGAAAGCGGACGCTGTTCTAAAAAAGGTCTCCTGCAGATC
 321 TGTCTGGGCTGTGATGACGAATATTATGAAATGTGCCTTTTCTGAAGAGATTGTGTTAGCTCCAAAGCTTTTCCTATCGC
 401 AGTGTTTCAGTTCTTTATTTTCCCTTGTGGATATGCTGTGTGAACCGTCGTGTGAGTGTGGTATGCCTGATCACAGATGG
 481 ATTTTGTTATAAGCATCAATGTGACACTTGCAGGACACTACAACGTGGGACATTGTTTGTTTCTTCCATATTTGGAAGAT
 561 AAATTTATGTGTAGACTTTTTTGTAAGATACGGTTAATAACTAAAATTTATTGAAATGGTCTTGCAATGACTCGTATTCA
 641 GATGCTTAAAGAAAGCATTGCTGCTACAAATATTTCTATTTTTAGAAAGGGTTTTTATGGACCAATGCCCCAGTTGTCAG
 721 TCAGAGCCGTTGGTGTTTTTCATTGTTTAAAATGTCACCTGTAAAATGGGCATTATTTATGTTTTTTTTTTTGCATTCCT
 801 GATAATTGTATGTATTGTATAAAGAACGTCTGTACATTGGGTTATAACACTAGTATATTTAAACTTACAGGCTTATTTGT
 881 AATGTAAACCACCATTTTAATGTACTGTAATTAACATGGTTATAATACGTACAATCCTTCCCTCATCCCATCACACAACT
 961 TTTTTTGTGTGTGATAAACTGATTTTGGTTTGCAATAAAACCTTGAAAAATATTTACATATAAAAAAAA
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' acuccguuuucauaccgUACCCGu 5'
                           |||||| 
Target 5' aaaatgtcacctgtaaaATGGGCa 3'
 749 - 772 120.00 -11.10
2 
miRNA  3' acucCGU--UUUCAUACCGUACCCgu 5'
              |||  | | ||   |:||||  
Target 5' acttGCAGGACACTACAACGTGGGac 3'
 506 - 531 114.00 -11.24
3 
miRNA  3' acucCGUUUUCAUACCGUACCCGu 5'
              |||:|  | || | ||||| 
Target 5' tcctGCAGA--TCTGTC-TGGGCt 3'
 310 - 330 108.00 -10.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26994521 53 COSMIC
COSN31523955 53 COSMIC
COSN30167455 60 COSMIC
COSN30104028 115 COSMIC
COSN31567234 147 COSMIC
COSN20705502 156 COSMIC
COSN26676976 209 COSMIC
COSN21171288 243 COSMIC
COSN30130155 254 COSMIC
COSN31522137 315 COSMIC
COSN15010832 339 COSMIC
COSN28628592 357 COSMIC
COSN30173276 398 COSMIC
COSN31582668 413 COSMIC
COSN9297750 591 COSMIC
COSN31591732 634 COSMIC
COSN31584617 639 COSMIC
COSN31519872 670 COSMIC
COSN19662937 781 COSMIC
COSN31607670 827 COSMIC
COSN26644620 905 COSMIC
COSN31611299 927 COSMIC
COSN26554018 932 COSMIC
COSN2142575 997 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs926570043 4 dbSNP
rs375654397 6 dbSNP
rs1341276634 7 dbSNP
rs768135465 19 dbSNP
rs527777726 23 dbSNP
rs774837183 28 dbSNP
rs1323999181 32 dbSNP
rs766810780 33 dbSNP
rs182230788 34 dbSNP
rs558510756 36 dbSNP
rs746511000 38 dbSNP
rs1172460528 41 dbSNP
rs372156281 43 dbSNP
rs548281620 44 dbSNP
rs745855329 47 dbSNP
rs1322144828 48 dbSNP
rs769476003 51 dbSNP
rs951165129 54 dbSNP
rs866243756 57 dbSNP
rs1026686420 64 dbSNP
rs1206978945 65 dbSNP
rs995006558 73 dbSNP
rs967334970 74 dbSNP
rs148282184 77 dbSNP
rs899292635 84 dbSNP
rs1039702524 88 dbSNP
rs1182033370 89 dbSNP
rs1007782376 98 dbSNP
rs1181474693 116 dbSNP
rs1424791128 116 dbSNP
rs1362587151 117 dbSNP
rs890470553 122 dbSNP
rs992678632 127 dbSNP
rs1160552175 134 dbSNP
rs1404799126 140 dbSNP
rs970447958 142 dbSNP
rs1338326073 145 dbSNP
rs144017729 146 dbSNP
rs1002330467 154 dbSNP
rs56006088 156 dbSNP
rs761573548 166 dbSNP
rs776360099 170 dbSNP
rs1223157014 171 dbSNP
rs1304515411 173 dbSNP
rs945346138 173 dbSNP
rs1350026285 179 dbSNP
rs1280280998 185 dbSNP
rs1282533546 188 dbSNP
rs1322971385 189 dbSNP
rs546453106 194 dbSNP
rs1258007718 195 dbSNP
rs577499411 208 dbSNP
rs761389375 213 dbSNP
rs866641295 215 dbSNP
rs914022265 219 dbSNP
rs749944895 220 dbSNP
rs1016974376 223 dbSNP
rs1248947510 228 dbSNP
rs1421240435 228 dbSNP
rs936490503 233 dbSNP
rs926441602 234 dbSNP
rs981115948 235 dbSNP
rs1479181383 236 dbSNP
rs189186128 238 dbSNP
rs949356453 239 dbSNP
rs746884554 242 dbSNP
rs537173165 243 dbSNP
rs1296080619 244 dbSNP
rs1377658222 245 dbSNP
rs1316786173 246 dbSNP
rs567739003 247 dbSNP
rs540516618 249 dbSNP
rs574980491 252 dbSNP
rs901371834 253 dbSNP
rs770903591 254 dbSNP
rs149522218 262 dbSNP
rs544339812 263 dbSNP
rs1249817232 266 dbSNP
rs942475922 268 dbSNP
rs80155856 271 dbSNP
rs74813322 272 dbSNP
rs1206248234 276 dbSNP
rs925677394 277 dbSNP
rs576227178 278 dbSNP
rs1026694612 287 dbSNP
rs913156358 291 dbSNP
rs558615801 292 dbSNP
rs56326915 293 dbSNP
rs963894699 293 dbSNP
rs554671835 298 dbSNP
rs1430193001 301 dbSNP
rs1302242187 305 dbSNP
rs1363644697 306 dbSNP
rs756458732 307 dbSNP
rs538910302 311 dbSNP
rs752993672 315 dbSNP
rs376144722 318 dbSNP
rs1368463934 322 dbSNP
rs1381690097 323 dbSNP
rs984139030 324 dbSNP
rs951424133 326 dbSNP
rs55894848 329 dbSNP
rs1229600963 334 dbSNP
rs890742040 336 dbSNP
rs1030579997 338 dbSNP
rs536015632 341 dbSNP
rs901405867 356 dbSNP
rs1485278038 364 dbSNP
rs796452787 371 dbSNP
rs1335811343 372 dbSNP
rs1184210184 393 dbSNP
rs11554162 396 dbSNP
rs1018411759 397 dbSNP
rs1006990782 398 dbSNP
rs1162537196 399 dbSNP
rs904284270 411 dbSNP
rs1426294512 413 dbSNP
rs892431016 415 dbSNP
rs1344482191 417 dbSNP
rs945809868 427 dbSNP
rs1430117610 436 dbSNP
rs1206924391 438 dbSNP
rs567136692 447 dbSNP
rs1292832039 449 dbSNP
rs548247037 450 dbSNP
rs62627406 451 dbSNP
rs979949576 455 dbSNP
rs1213042723 465 dbSNP
rs1407763018 465 dbSNP
rs936739354 469 dbSNP
rs941801174 470 dbSNP
rs186276516 476 dbSNP
rs1357748854 488 dbSNP
rs180843823 490 dbSNP
rs1044936431 496 dbSNP
rs547421321 499 dbSNP
rs1398945010 501 dbSNP
rs951493598 508 dbSNP
rs949236564 511 dbSNP
rs976765705 514 dbSNP
rs917875235 516 dbSNP
rs1404116078 521 dbSNP
rs1165176861 523 dbSNP
rs79927819 524 dbSNP
rs188810026 525 dbSNP
rs929653261 527 dbSNP
rs775535692 528 dbSNP
rs763842021 529 dbSNP
rs1417088197 530 dbSNP
rs1185763843 534 dbSNP
rs1475631591 543 dbSNP
rs1329292932 546 dbSNP
rs1018444269 550 dbSNP
rs1260877218 569 dbSNP
rs1443716658 570 dbSNP
rs1210376993 582 dbSNP
rs1007021662 583 dbSNP
rs1232143498 583 dbSNP
rs904735039 587 dbSNP
rs919565678 591 dbSNP
rs7754021 592 dbSNP
rs1175730364 606 dbSNP
rs1010427665 610 dbSNP
rs759800888 611 dbSNP
rs1335090731 616 dbSNP
rs1354371150 624 dbSNP
rs1440433209 625 dbSNP
rs1310424478 627 dbSNP
rs865786709 633 dbSNP
rs1018427123 634 dbSNP
rs1272690483 639 dbSNP
rs1346487470 640 dbSNP
rs1214552195 643 dbSNP
rs1271811908 650 dbSNP
rs1435896282 656 dbSNP
rs1165802746 663 dbSNP
rs1337280566 669 dbSNP
rs986350031 670 dbSNP
rs1252468167 672 dbSNP
rs1271301396 673 dbSNP
rs1197188220 678 dbSNP
rs1214306328 683 dbSNP
rs1376053409 685 dbSNP
rs955042423 689 dbSNP
rs1479037855 690 dbSNP
rs1173418692 698 dbSNP
rs938335946 700 dbSNP
rs1428250751 703 dbSNP
rs1363093083 705 dbSNP
rs905779744 706 dbSNP
rs1030589452 708 dbSNP
rs1404938789 722 dbSNP
rs184076667 724 dbSNP
rs1399564170 725 dbSNP
rs1436521243 728 dbSNP
rs1269252265 736 dbSNP
rs532938039 743 dbSNP
rs1336978992 745 dbSNP
rs1044300082 752 dbSNP
rs1358449802 762 dbSNP
rs1009786686 773 dbSNP
rs892482209 774 dbSNP
rs1032318568 781 dbSNP
rs1326041057 781 dbSNP
rs530282561 782 dbSNP
rs1170699766 793 dbSNP
rs1391217645 793 dbSNP
rs1453434778 793 dbSNP
rs55984236 793 dbSNP
rs774779984 794 dbSNP
rs1169345359 795 dbSNP
rs1162010104 796 dbSNP
rs1410258739 798 dbSNP
rs1421407956 799 dbSNP
rs930079226 804 dbSNP
rs561489664 813 dbSNP
rs1316935054 815 dbSNP
rs918656910 816 dbSNP
rs977161536 818 dbSNP
rs965315688 819 dbSNP
rs58321558 828 dbSNP
rs1242291414 834 dbSNP
rs1267175211 835 dbSNP
rs1356895955 836 dbSNP
rs1045556306 841 dbSNP
rs1204471408 846 dbSNP
rs3836933 851 dbSNP
rs118055987 853 dbSNP
rs1283718295 853 dbSNP
rs75591900 855 dbSNP
rs1204103754 864 dbSNP
rs1248835616 865 dbSNP
rs544727374 868 dbSNP
rs1022241400 869 dbSNP
rs572802400 881 dbSNP
rs764749703 885 dbSNP
rs1473451180 894 dbSNP
rs1158483434 898 dbSNP
rs1385871358 905 dbSNP
rs552954115 907 dbSNP
rs1320850850 916 dbSNP
rs919824194 928 dbSNP
rs536567255 929 dbSNP
rs1038067168 934 dbSNP
rs942352430 935 dbSNP
rs1370546418 950 dbSNP
rs771278977 954 dbSNP
rs141074164 959 dbSNP
rs556770232 961 dbSNP
rs1210614803 967 dbSNP
rs1269021724 967 dbSNP
rs34857215 967 dbSNP
rs550125547 967 dbSNP
rs1006165586 976 dbSNP
rs1198941313 976 dbSNP
rs1258771163 977 dbSNP
rs887686797 978 dbSNP
rs1048034684 985 dbSNP
rs761413514 986 dbSNP
rs773172955 987 dbSNP
rs986913489 992 dbSNP
rs537936536 1002 dbSNP
rs1428174755 1013 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

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

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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000367858.5 | 3UTR | GUGUUUUUCAUUGUUUAAAAUGUCACCUGUAAAAUGGGCAUUAUUUAUGUUUUUUUUUUUGCAUUCCUG
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
47 hsa-miR-4641 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT082839 ZNF460 zinc finger protein 460 2 6
MIRT153778 NCOA3 nuclear receptor coactivator 3 2 2
MIRT168563 HMGA1 high mobility group AT-hook 1 2 2
MIRT192245 BTF3L4 basic transcription factor 3 like 4 2 4
MIRT195168 PAPD5 poly(A) RNA polymerase D5, non-canonical 2 4
MIRT233689 IGF1R insulin like growth factor 1 receptor 2 2
MIRT256315 CDC42SE2 CDC42 small effector 2 2 2
MIRT277105 CDCA8 cell division cycle associated 8 2 2
MIRT358532 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B 2 2
MIRT452315 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT454556 WARS tryptophanyl-tRNA synthetase 2 2
MIRT465518 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT468196 SGK1 serum/glucocorticoid regulated kinase 1 2 2
MIRT473446 MCOLN2 mucolipin 2 2 8
MIRT478074 DNAJB4 DnaJ heat shock protein family (Hsp40) member B4 2 2
MIRT494943 IFFO2 intermediate filament family orphan 2 2 2
MIRT495545 ANKRD65 ankyrin repeat domain 65 2 2
MIRT501671 PFN1 profilin 1 2 8
MIRT506311 PANK3 pantothenate kinase 3 2 4
MIRT507871 CBX6 chromobox 6 2 2
MIRT514031 BNIP2 BCL2 interacting protein 2 2 2
MIRT527792 KLRD1 killer cell lectin like receptor D1 2 2
MIRT529896 C1orf64 steroid receptor associated and regulated protein 2 2
MIRT546702 RORA RAR related orphan receptor A 2 4
MIRT554220 SLC2A3 solute carrier family 2 member 3 2 2
MIRT554253 SIX4 SIX homeobox 4 2 2
MIRT557722 G3BP1 G3BP stress granule assembly factor 1 2 2
MIRT573043 SHMT1 serine hydroxymethyltransferase 1 2 2
MIRT573998 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 2 2
MIRT574694 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT611607 AQP3 aquaporin 3 (Gill blood group) 2 2
MIRT624505 C7orf73 short transmembrane mitochondrial protein 1 2 2
MIRT630620 CXCR6 C-X-C motif chemokine receptor 6 2 2
MIRT634862 FSIP2 fibrous sheath interacting protein 2 2 2
MIRT640371 UQCRB ubiquinol-cytochrome c reductase binding protein 2 2
MIRT641515 CREBBP CREB binding protein 2 2
MIRT645031 DVL1 dishevelled segment polarity protein 1 2 2
MIRT649688 SLC1A1 solute carrier family 1 member 1 2 2
MIRT665113 DNASE2 deoxyribonuclease 2, lysosomal 2 2
MIRT700687 POLR3D RNA polymerase III subunit D 2 2
MIRT703456 FTO FTO, alpha-ketoglutarate dependent dioxygenase 2 2
MIRT705286 B4GALT1 beta-1,4-galactosyltransferase 1 2 2
MIRT708277 ZNF101 zinc finger protein 101 2 2
MIRT709670 AJAP1 adherens junctions associated protein 1 2 2
MIRT712896 TGFA transforming growth factor alpha 2 2
MIRT717596 PHLDA3 pleckstrin homology like domain family A member 3 2 2
MIRT719008 TMEM184C transmembrane protein 184C 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4641 Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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