miRTarBase - #MIRT480639


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pre-miRNA Information
pre-miRNA hsa-mir-4316   
Genomic Coordinates chr17: 77396984 - 77397054
Description Homo sapiens miR-4316 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4316
Sequence 11| GGUGAGGCUAGCUGGUG |27
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs989002279 5 dbSNP
rs957742923 17 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol BSCL2   
Synonyms GNG3LG, HMN5, PELD, SPG17
Description BSCL2, seipin lipid droplet biogenesis associated
Transcript NM_001130702   
Other Transcripts NM_001122955 , NM_032667   
Expression
Putative miRNA Targets on BSCL2
3'UTR of BSCL2
(miRNA target sites are highlighted)		 
>BSCL2|NM_001130702|3'UTR
   1 GCGGAGAAGAGGAGCTAGAGCCTGAGGCCAGTGATGGTTCAGGCTCCTGGGAAGATGCAGCTTTGCTGACGGAGGCCAAC
  81 CTGCCTGCTCCTGCTCCTGCTTCTGCTTCTGCCCCTGTCCTAGAGACTCTGGGCAGCTCTGAACCTGCTGGGGGTGCTCT
 161 CCGACAGCGCCCCACCTGCTCTAGTTCCTGAAGAAAAGGGGCAGACTCCTCACATTCCAGCACTTTCCCACCTGACTCCT
 241 CTCCCCTCGTTTTTCCTTCAATAAACTATTTTGTGTCAGCTTCTTCCTTGACTCTG
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' gugGUC-GAUCGGAGUGg 5'
             ||| ||  |||||| 
Target 5' gggCAGACT--CCTCACa 3'
 199 - 214 121.00 -12.80
2 
miRNA  3' gugGUCGAUCGGAGUGg 5'
             ||||  ||| ||| 
Target 5' cgaCAGC--GCCCCACc 3'
 162 - 176 118.00 -14.40
3 
miRNA  3' guggUCGA--UCGGAGUgg 5'
              ||||  ||||| |  
Target 5' gaggAGCTAGAGCCTGAgg 3'
 9 - 27 103.00 -8.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
879418 2 ClinVar
245798 3 ClinVar
567989 4 ClinVar
799731 14 ClinVar
696445 15 ClinVar
663994 42 ClinVar
509292 43 ClinVar
305173 50 ClinVar
509502 55 ClinVar
1118997 121 ClinVar
623295 125 ClinVar
660054 136 ClinVar
1080520 143 ClinVar
543282 146 ClinVar
1051573 160 ClinVar
543171 168 ClinVar
128532 172 ClinVar
387999 174 ClinVar
241723 180 ClinVar
566241 190 ClinVar
943575 192 ClinVar
951620 192 ClinVar
234752 201 ClinVar
1117396 203 ClinVar
393431 203 ClinVar
646533 203 ClinVar
937593 205 ClinVar
369947 209 ClinVar
795252 212 ClinVar
234682 217 ClinVar
999392 244 ClinVar
411580 246 ClinVar
1032980 252 ClinVar
388768 253 ClinVar
193938 259 ClinVar
806685 261 ClinVar
938139 265 ClinVar
759768 266 ClinVar
835390 268 ClinVar
947075 279 ClinVar
305172 330 ClinVar
877793 339 ClinVar
COSM3451068 8 COSMIC
COSM3986305 11 COSMIC
COSM929788 22 COSMIC
COSM3809861 24 COSMIC
COSN30550896 70 COSMIC
COSM8762183 131 COSMIC
COSM8391958 133 COSMIC
COSM9581865 136 COSMIC
COSM8209913 156 COSMIC
COSM3687774 160 COSMIC
COSM8240626 161 COSMIC
COSM9507854 170 COSMIC
COSM1492621 203 COSMIC
COSM9655061 203 COSMIC
COSM8389780 210 COSMIC
COSM9128759 222 COSMIC
COSM8490413 230 COSMIC
COSM3980507 243 COSMIC
COSM2039478 252 COSMIC
COSM6613138 253 COSMIC
COSM7785712 278 COSMIC
COSN31560098 307 COSMIC
COSN30509624 319 COSMIC
COSN30514158 331 COSMIC
COSN30180818 334 COSMIC
COSN30187993 340 COSMIC
COSN30109445 373 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs766492897 2 dbSNP
rs138964424 3 dbSNP
rs767463971 4 dbSNP
rs1333743966 9 dbSNP
rs563653317 14 dbSNP
rs556562410 15 dbSNP
rs1190940122 16 dbSNP
rs1173283308 20 dbSNP
rs925294616 22 dbSNP
rs774201363 27 dbSNP
rs1181465202 31 dbSNP
rs768191284 32 dbSNP
rs762726296 42 dbSNP
rs200631909 43 dbSNP
rs369813738 47 dbSNP
rs374197154 48 dbSNP
rs778380128 50 dbSNP
rs957573465 51 dbSNP
rs748453195 55 dbSNP
rs113229350 56 dbSNP
rs1239072478 60 dbSNP
rs147311459 69 dbSNP
rs755130483 70 dbSNP
rs1311305069 71 dbSNP
rs780284832 72 dbSNP
rs1236748653 74 dbSNP
rs547938973 75 dbSNP
rs370410858 76 dbSNP
rs201532363 87 dbSNP
rs769506704 89 dbSNP
rs998320931 92 dbSNP
rs1307198436 93 dbSNP
rs751300763 102 dbSNP
rs1382982511 106 dbSNP
rs1158243926 108 dbSNP
rs764000384 110 dbSNP
rs1376332102 114 dbSNP
rs1382538396 117 dbSNP
rs1162110568 119 dbSNP
rs762484263 121 dbSNP
rs775246044 123 dbSNP
rs113937239 124 dbSNP
rs1187561826 127 dbSNP
rs768646836 143 dbSNP
rs759063057 145 dbSNP
rs776343859 146 dbSNP
rs1354030991 151 dbSNP
rs772442281 156 dbSNP
rs1272067091 158 dbSNP
rs1266361176 160 dbSNP
rs748736063 161 dbSNP
rs779114853 163 dbSNP
rs769023011 166 dbSNP
rs1450251165 169 dbSNP
rs1197237474 171 dbSNP
rs145649423 172 dbSNP
rs369732238 174 dbSNP
rs1004545791 178 dbSNP
rs1383028616 179 dbSNP
rs377310581 180 dbSNP
rs1362768761 188 dbSNP
rs1052004305 189 dbSNP
rs141657385 190 dbSNP
rs199584887 192 dbSNP
rs771054711 192 dbSNP
rs776687260 192 dbSNP
rs1045933 193 dbSNP
rs199787351 201 dbSNP
rs751558047 202 dbSNP
rs747175358 203 dbSNP
rs778093697 203 dbSNP
rs763972632 204 dbSNP
rs1473465067 205 dbSNP
rs1370817987 206 dbSNP
rs1057516190 209 dbSNP
rs376418772 212 dbSNP
rs1045944 213 dbSNP
rs1313898247 215 dbSNP
rs876661160 217 dbSNP
rs1488410118 222 dbSNP
rs1264900374 224 dbSNP
rs1323940047 226 dbSNP
rs752558297 227 dbSNP
rs3185964 229 dbSNP
rs772211936 229 dbSNP
rs764974038 230 dbSNP
rs1200019034 231 dbSNP
rs1235176988 232 dbSNP
rs1229941132 233 dbSNP
rs748492948 234 dbSNP
rs1337416976 237 dbSNP
rs759317218 242 dbSNP
rs779952369 244 dbSNP
rs1060503382 246 dbSNP
rs1257836442 248 dbSNP
rs1426557167 251 dbSNP
rs138515091 252 dbSNP
rs143017094 253 dbSNP
rs529970386 257 dbSNP
rs149466797 259 dbSNP
rs769048111 261 dbSNP
rs749597554 263 dbSNP
rs775890636 268 dbSNP
rs3186041 271 dbSNP
rs769997563 274 dbSNP
rs746128300 275 dbSNP
rs112311529 279 dbSNP
rs779154593 279 dbSNP
rs538682035 299 dbSNP
rs1247038766 301 dbSNP
rs755542483 303 dbSNP
rs945376749 304 dbSNP
rs757310587 305 dbSNP
rs1199275011 307 dbSNP
rs927876804 316 dbSNP
rs747087493 322 dbSNP
rs1218843697 325 dbSNP
rs777695987 327 dbSNP
rs1276968323 328 dbSNP
rs576081892 329 dbSNP
rs368144792 330 dbSNP
rs765167711 331 dbSNP
rs374017840 333 dbSNP
rs1401816370 334 dbSNP
rs535829182 335 dbSNP
rs913329942 336 dbSNP
rs567462672 338 dbSNP
rs755714656 339 dbSNP
rs764649212 340 dbSNP
rs763517904 351 dbSNP
rs775798921 352 dbSNP
rs1487073806 353 dbSNP
rs957459239 355 dbSNP
rs1179201523 358 dbSNP
rs566951883 359 dbSNP
rs1261300820 362 dbSNP
rs1209589243 363 dbSNP
rs770191886 365 dbSNP
rs1281003364 370 dbSNP
rs1222385132 374 dbSNP
rs1429120136 376 dbSNP
rs1353469506 379 dbSNP
rs1310515312 382 dbSNP
rs749872089 387 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.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' guggucgaucGGAGUGg 5'
                    |||||| 
Target 5' -------acuCCUCACa 3'
 		1 - 10
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 GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_001130702 | 3UTR | CAGACUCCUCACAUUCCAGCACUUUCCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000278893.7 | 3UTR | ACUCCUCACAUUCCAGCACUUUCCCACCUG
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
74 hsa-miR-4316 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT080624 PMAIP1 phorbol-12-myristate-13-acetate-induced protein 1 2 2
MIRT095088 SEC24A SEC24 homolog A, COPII coat complex component 2 4
MIRT123331 CALU calumenin 2 2
MIRT154964 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT370850 TGFBR2 transforming growth factor beta receptor 2 2 2
MIRT442955 SGCD sarcoglycan delta 2 2
MIRT448240 ZNF774 zinc finger protein 774 2 2
MIRT451710 OLR1 oxidized low density lipoprotein receptor 1 2 2
MIRT452072 ATP6V0B ATPase H+ transporting V0 subunit b 2 2
MIRT455665 GLO1 glyoxalase I 2 2
MIRT460354 TXNDC16 thioredoxin domain containing 16 2 2
MIRT461908 NECAB3 N-terminal EF-hand calcium binding protein 3 2 2
MIRT462047 HOXC13 homeobox C13 2 2
MIRT462735 EFNB1 ephrin B1 2 2
MIRT463409 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT464952 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT465052 TSR1 TSR1, ribosome maturation factor 2 2
MIRT467549 SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 2 4
MIRT470226 PRRC2A proline rich coiled-coil 2A 2 2
MIRT474081 LMBR1L limb development membrane protein 1 like 2 2
MIRT474481 KLHDC8B kelch domain containing 8B 2 2
MIRT474704 KIF3A kinesin family member 3A 2 2
MIRT474897 KCTD21 potassium channel tetramerization domain containing 21 2 2
MIRT475203 IL2RB interleukin 2 receptor subunit beta 2 2
MIRT477664 EFHD2 EF-hand domain family member D2 2 2
MIRT477775 E2F3 E2F transcription factor 3 2 2
MIRT477940 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT478224 DDX52 DExD-box helicase 52 2 2
MIRT479904 CCDC117 coiled-coil domain containing 117 2 2
MIRT480639 BSCL2 BSCL2, seipin lipid droplet biogenesis associated 2 2
MIRT482435 ADM adrenomedullin 2 10
MIRT483908 GNB1L G protein subunit beta 1 like 2 2
MIRT484161 FAM71B family with sequence similarity 71 member B 2 2
MIRT484405 SNX19 sorting nexin 19 2 2
MIRT485426 LASP1 LIM and SH3 protein 1 2 2
MIRT489788 KRT80 keratin 80 2 4
MIRT490813 ASB1 ankyrin repeat and SOCS box containing 1 2 4
MIRT491176 LAMA5 laminin subunit alpha 5 2 2
MIRT491573 HSDL1 hydroxysteroid dehydrogenase like 1 2 2
MIRT492633 PLXNA1 plexin A1 2 2
MIRT492984 NAV1 neuron navigator 1 2 2
MIRT496441 RAB11FIP4 RAB11 family interacting protein 4 2 2
MIRT501829 NCOA3 nuclear receptor coactivator 3 2 2
MIRT502165 KIAA0195 transmembrane protein 94 2 2
MIRT508652 DIABLO diablo IAP-binding mitochondrial protein 2 4
MIRT509554 ACTG1 actin gamma 1 2 4
MIRT520033 YOD1 YOD1 deubiquitinase 2 6
MIRT523969 DVL3 dishevelled segment polarity protein 3 2 2
MIRT526150 KIAA1456 KIAA1456 2 2
MIRT530330 ARHGAP1 Rho GTPase activating protein 1 2 2
MIRT539985 SLC24A4 solute carrier family 24 member 4 2 4
MIRT540851 NUP155 nucleoporin 155 2 2
MIRT542326 LIMD1 LIM domains containing 1 2 2
MIRT558908 CBX5 chromobox 5 2 2
MIRT563663 SMC4 structural maintenance of chromosomes 4 2 2
MIRT565433 SURF4 surfeit 4 2 2
MIRT567773 DGAT2 diacylglycerol O-acyltransferase 2 2 2
MIRT615573 NCS1 neuronal calcium sensor 1 2 2
MIRT627336 TTLL7 tubulin tyrosine ligase like 7 2 2
MIRT632965 EIF2S3 eukaryotic translation initiation factor 2 subunit gamma 2 2
MIRT634307 SNTN sentan, cilia apical structure protein 2 2
MIRT641569 RAX retina and anterior neural fold homeobox 2 2
MIRT660509 ARL5A ADP ribosylation factor like GTPase 5A 2 2
MIRT662703 C10orf111 chromosome 10 open reading frame 111 2 4
MIRT663214 ZNF277 zinc finger protein 277 2 2
MIRT665318 YIPF4 Yip1 domain family member 4 2 2
MIRT695264 CD209 CD209 molecule 2 2
MIRT696231 LIN9 lin-9 DREAM MuvB core complex component 2 2
MIRT698867 SRPR SRP receptor alpha subunit 2 2
MIRT702700 IPO9 importin 9 2 2
MIRT704236 DHDDS dehydrodolichyl diphosphate synthase subunit 2 2
MIRT704935 CCDC120 coiled-coil domain containing 120 2 2
MIRT724285 KCNMB1 potassium calcium-activated channel subfamily M regulatory beta subunit 1 2 2
MIRT735579 VEGFA vascular endothelial growth factor A 3 0
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-4316 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-miR-4316 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4316 Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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