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 FAM71B   
Synonyms -
Description family with sequence similarity 71 member B
Transcript NM_130899   
Expression
Putative miRNA Targets on FAM71B
3'UTR of FAM71B
(miRNA target sites are highlighted)
>FAM71B|NM_130899|3'UTR
   1 AGAGGAGCCAGGGCTACAACCGCCCAGGGATCTGGAAGTATCCCTAGAGGAGCCCATCCCAGCTTTCTTTACTGCAGTTC
  81 AAATAATAAAGGAAATCGTACAACTCCAAAAGAAAAAAAAAAAAAAAA
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' guGGUCGAUCGGAGUGg 5'
            ||||||  |:|:|| 
Target 5' tcCCAGCTTTCTTTACt 3'
57 - 73 103.00 -15.30
2
miRNA  3' guGGUCGAUCGGAGUgg 5'
            ||||  :||: ||  
Target 5' agCCAG--GGCTACAac 3'
6 - 20 83.00 -7.90
3
miRNA  3' guGGUC----GA---UCGGAGUGg 5'
            ||||    ||   ||: || | 
Target 5' gcCCAGGGATCTGGAAGTATCCCt 3'
22 - 45 69.00 -11.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30457524 5 COSMIC
COSN31485101 5 COSMIC
COSN30491797 14 COSMIC
COSN30181890 17 COSMIC
COSN30504138 21 COSMIC
COSN14151744 22 COSMIC
COSN31577452 27 COSMIC
COSN30472159 28 COSMIC
COSN30192548 47 COSMIC
COSN20064053 48 COSMIC
COSN30462995 50 COSMIC
COSN15315612 59 COSMIC
COSN31607371 67 COSMIC
COSN30120424 92 COSMIC
COSN19706949 97 COSMIC
COSN14151741 98 COSMIC
COSN30518789 101 COSMIC
COSN28691236 166 COSMIC
COSN9413863 181 COSMIC
COSN25905909 243 COSMIC
COSN15056499 389 COSMIC
COSN2079635 451 COSMIC
COSN24839703 556 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1047845304 4 dbSNP
rs1351627574 7 dbSNP
rs995298335 8 dbSNP
rs369804995 13 dbSNP
rs750592442 14 dbSNP
rs1366840968 15 dbSNP
rs779120509 16 dbSNP
rs1163387185 17 dbSNP
rs550645272 20 dbSNP
rs754225436 21 dbSNP
rs764423052 22 dbSNP
rs531731172 23 dbSNP
rs761214256 24 dbSNP
rs1267928506 28 dbSNP
rs1197136331 29 dbSNP
rs1490825523 30 dbSNP
rs753288128 35 dbSNP
rs1435528459 37 dbSNP
rs1210549262 39 dbSNP
rs767088416 40 dbSNP
rs759132386 44 dbSNP
rs899180691 45 dbSNP
rs1233946623 50 dbSNP
rs370147732 52 dbSNP
rs1039423415 53 dbSNP
rs943356286 54 dbSNP
rs2278385 59 dbSNP
rs1406954557 67 dbSNP
rs907699503 68 dbSNP
rs574910592 70 dbSNP
rs1051624189 75 dbSNP
rs945251747 84 dbSNP
rs1338673807 85 dbSNP
rs201548920 85 dbSNP
rs1409427824 94 dbSNP
rs913685883 96 dbSNP
rs575674872 97 dbSNP
rs557628807 98 dbSNP
rs957998121 99 dbSNP
rs1347537223 101 dbSNP
rs1174495733 103 dbSNP
rs1469630268 107 dbSNP
rs926327307 112 dbSNP
rs1354533170 118 dbSNP
rs371496027 122 dbSNP
rs546229268 139 dbSNP
rs1202002395 145 dbSNP
rs1337098785 149 dbSNP
rs1213467984 152 dbSNP
rs1273181071 154 dbSNP
rs1308757825 156 dbSNP
rs1209291615 158 dbSNP
rs1235234065 174 dbSNP
rs975516007 185 dbSNP
rs964022608 189 dbSNP
rs970367944 190 dbSNP
rs144687161 191 dbSNP
rs1014509586 195 dbSNP
rs1485869326 204 dbSNP
rs1168719054 206 dbSNP
rs950871778 207 dbSNP
rs112300940 208 dbSNP
rs35421005 210 dbSNP
rs139778518 217 dbSNP
rs1263578463 227 dbSNP
rs1011709833 232 dbSNP
rs575125355 237 dbSNP
rs1039105823 238 dbSNP
rs555240369 243 dbSNP
rs538108881 244 dbSNP
rs1382853922 247 dbSNP
rs1349305982 249 dbSNP
rs1051635460 259 dbSNP
rs535184941 260 dbSNP
rs1446799819 266 dbSNP
rs892312747 268 dbSNP
rs1054003766 269 dbSNP
rs31207 270 dbSNP
rs1049463055 272 dbSNP
rs930441594 281 dbSNP
rs926393102 282 dbSNP
rs538267419 283 dbSNP
rs566206389 298 dbSNP
rs146089215 299 dbSNP
rs1464383278 300 dbSNP
rs1370986350 309 dbSNP
rs1318530149 311 dbSNP
rs1366973665 315 dbSNP
rs1302141630 317 dbSNP
rs534780522 318 dbSNP
rs1235994949 325 dbSNP
rs980507894 328 dbSNP
rs949069405 339 dbSNP
rs986778146 342 dbSNP
rs1286584828 351 dbSNP
rs536030881 356 dbSNP
rs567398810 357 dbSNP
rs764172642 367 dbSNP
rs1200856753 370 dbSNP
rs1455654944 370 dbSNP
rs375247484 373 dbSNP
rs530676798 380 dbSNP
rs778260014 384 dbSNP
rs913454016 386 dbSNP
rs762809997 391 dbSNP
rs990380033 392 dbSNP
rs1390393150 397 dbSNP
rs1459608575 408 dbSNP
rs1026550077 413 dbSNP
rs1324788617 415 dbSNP
rs1394644579 439 dbSNP
rs1387976483 441 dbSNP
rs1034507567 447 dbSNP
rs1181184635 448 dbSNP
rs567727542 449 dbSNP
rs1290522244 454 dbSNP
rs1333139499 456 dbSNP
rs58699522 471 dbSNP
rs1205402467 477 dbSNP
rs1315763409 482 dbSNP
rs1250984370 483 dbSNP
rs1274013232 488 dbSNP
rs1024484767 491 dbSNP
rs1194104754 498 dbSNP
rs1248346548 504 dbSNP
rs552577497 518 dbSNP
rs1182433796 519 dbSNP
rs1413983239 526 dbSNP
rs1004524530 531 dbSNP
rs532584486 532 dbSNP
rs1228374552 535 dbSNP
rs748487667 541 dbSNP
rs560289595 551 dbSNP
rs1418073576 556 dbSNP
rs886124445 561 dbSNP
rs1295885798 562 dbSNP
rs1396414515 566 dbSNP
rs1027555833 567 dbSNP
rs1310370609 569 dbSNP
rs1354003992 570 dbSNP
rs1414512434 572 dbSNP
rs1294163636 582 dbSNP
rs1323673403 586 dbSNP
rs1007560461 592 dbSNP
rs890463856 599 dbSNP
rs1310729603 601 dbSNP
rs994787316 602 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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000302938.4 | 3UTR | CUCACAGUGGCUUCUGU
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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