pre-miRNA Information
pre-miRNA hsa-mir-4280   
Genomic Coordinates chr5: 87114879 - 87114954
Description Homo sapiens miR-4280 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4280
Sequence 11| GAGUGUAGUUCUGAGCAGAGC |31
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1267452683 6 dbSNP
rs921418201 13 dbSNP
rs975577876 15 dbSNP
rs562687273 20 dbSNP
rs968639930 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PPIL4   
Synonyms HDCME13P
Description peptidylprolyl isomerase like 4
Transcript NM_139126   
Expression
Putative miRNA Targets on PPIL4
3'UTR of PPIL4
(miRNA target sites are highlighted)
>PPIL4|NM_139126|3'UTR
   1 AAGATGAAGAGGCAGAATTGAGAGGCTAACATATTTACTCTTGTCTAACTTAAGAGTGCCAGGAAAGCAGATGCTTAGAT
  81 TTTGTGTCAAAGCTTGTTATTTTTTTCATACTAGGATTATGGTCTTTAGATTAATACTGATTATATAGAGCACGGAAAGA
 161 TAAAGAATTGAACATTTTCTTTGTATACTTTTTTACACTAATTTTATTGTTATACATAAATGGTAGTCTTCATTTTTGAA
 241 GTCTTACATTTTCACTCTTTTTTTAATGAAGTATTTCATACTACAAAAATACATAAACGTATATATAAAGGGATAATAAA
 321 TGTAAATATCTGTGTACTCATCAGCCAGCTTAAGATACAGATGTTGTCGACATTTTAGAAGTTCCCTAAGGCCCTCTCCC
 401 TCTCAAATAATTATTTGGAATTTTGTGTTTGTCATTTGTCTATTATAGTTTTACAACATACGTATGTATCTGTAAGTGAA
 481 ATGTTAATTTTGTATGTTTCTGAATTTTATATAAATGGCAAAATGTTTACTTCTGTGACTTTCTTTCATTTTTATTGCTA
 561 TATAGTATTATATAAATATACTACAACTTATTCATTCTTGATGGACATTTGAGTTTTGTTTATTTGTTTTTGCTGTTGAA
 641 ACAATGCTGCTGTGAACATTGTATCTAGCAGTTATATTGCTTGATATATTGATAAAATAATGCCAAATTTGTGTTCTGAA
 721 GTGACTGTACTAGTTTATACCTCTCTTGGCACTGTGAGTTACCTTTGTTTCATAGCATCTCCAACACTTAAGTTCAGACT
 801 TAAAAATTTGCCAACCTAGTGGATGTTAAGTGGTATCTACCTGTGATTTCCAGCAAGATTACTGTTATCTCTGCTCTTCC
 881 ATGTGTAAGATGTCATTTTTTTCCTGGCTGCTTTTAAGGTTTTCTGTCACTGGTTGTAAGAAGTTTGATTATGATGTGAA
 961 AAAAAAAAAAAA
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' cgAGACGAGUCU----UGAUGUGAg 5'
            | ||:|| ||    |||::||| 
Target 5' ttTGTGTTCTGAAGTGACTGTACTa 3'
708 - 732 129.00 -16.30
2
miRNA  3' cgAGACGAGUCUU-------GAUGUGAg 5'
            |:| ||: | |       :|||||| 
Target 5' caTTTTCTTTGTATACTTTTTTACACTa 3'
173 - 200 127.00 -11.00
3
miRNA  3' cgAGACGAGUCUU---GAUGUGAg 5'
            ||  :|: |||   :||||:| 
Target 5' ctTCATTTTTGAAGTCTTACATTt 3'
228 - 251 119.00 -9.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30111388 18 COSMIC
COSN30123828 27 COSMIC
COSN30165811 31 COSMIC
COSN30529174 101 COSMIC
COSN31510595 128 COSMIC
COSN30177399 146 COSMIC
COSN31543655 150 COSMIC
COSN30536628 164 COSMIC
COSN31585455 204 COSMIC
COSN16958302 462 COSMIC
COSN20966474 593 COSMIC
COSN7694032 613 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs374807873 3 dbSNP
rs776224862 4 dbSNP
rs770368270 18 dbSNP
rs760173897 24 dbSNP
rs774724138 26 dbSNP
rs199529936 29 dbSNP
rs1474724429 30 dbSNP
rs1188278282 31 dbSNP
rs1355756168 35 dbSNP
rs749724789 38 dbSNP
rs1451549197 44 dbSNP
rs750765344 54 dbSNP
rs772233371 70 dbSNP
rs545991228 84 dbSNP
rs1405971415 90 dbSNP
rs575461000 97 dbSNP
rs1237108405 107 dbSNP
rs561855961 108 dbSNP
rs1013931820 110 dbSNP
rs1041681459 115 dbSNP
rs542021908 129 dbSNP
rs1243312517 137 dbSNP
rs1313833967 143 dbSNP
rs189949323 148 dbSNP
rs1211056449 153 dbSNP
rs74367049 154 dbSNP
rs1445741402 158 dbSNP
rs1015173672 164 dbSNP
rs1249036376 165 dbSNP
rs1182149913 173 dbSNP
rs1451651787 173 dbSNP
rs1004554627 174 dbSNP
rs1473268053 175 dbSNP
rs1165045757 179 dbSNP
rs931960077 185 dbSNP
rs1439730411 188 dbSNP
rs1456627640 204 dbSNP
rs779340888 213 dbSNP
rs976184920 216 dbSNP
rs1450114002 226 dbSNP
rs1290265001 248 dbSNP
rs887560777 248 dbSNP
rs1027275923 253 dbSNP
rs966640268 257 dbSNP
rs1451070562 259 dbSNP
rs1344069708 260 dbSNP
rs908031832 260 dbSNP
rs1269260067 261 dbSNP
rs1466658839 264 dbSNP
rs566294499 265 dbSNP
rs900071496 266 dbSNP
rs1443193510 274 dbSNP
rs983558874 281 dbSNP
rs1039927309 289 dbSNP
rs952306966 298 dbSNP
rs553095625 299 dbSNP
rs1414030112 300 dbSNP
rs974185058 303 dbSNP
rs1468193912 310 dbSNP
rs1449837599 311 dbSNP
rs1171745771 321 dbSNP
rs1264194650 331 dbSNP
rs768984800 334 dbSNP
rs958391704 340 dbSNP
rs149457606 343 dbSNP
rs1397400730 348 dbSNP
rs1326373919 356 dbSNP
rs1349514748 362 dbSNP
rs115247701 368 dbSNP
rs1002610607 369 dbSNP
rs906930773 377 dbSNP
rs1020144820 384 dbSNP
rs1052614279 386 dbSNP
rs1231769608 408 dbSNP
rs1255757066 410 dbSNP
rs1256627795 426 dbSNP
rs1202547776 427 dbSNP
rs7773304 439 dbSNP
rs925381570 440 dbSNP
rs1182937509 458 dbSNP
rs781007895 458 dbSNP
rs979413024 459 dbSNP
rs1198143764 461 dbSNP
rs1054369616 462 dbSNP
rs1467340006 466 dbSNP
rs1165965839 467 dbSNP
rs536666336 469 dbSNP
rs916587295 471 dbSNP
rs1309293333 474 dbSNP
rs932009535 478 dbSNP
rs137953320 479 dbSNP
rs1040881781 481 dbSNP
rs1332192580 494 dbSNP
rs944827092 502 dbSNP
rs1328553975 509 dbSNP
rs907931927 511 dbSNP
rs991361408 517 dbSNP
rs554875035 519 dbSNP
rs1341681043 529 dbSNP
rs1297336408 535 dbSNP
rs1276843562 537 dbSNP
rs1380139280 542 dbSNP
rs1487582310 545 dbSNP
rs1209337236 547 dbSNP
rs548077454 548 dbSNP
rs879517603 549 dbSNP
rs1312890330 552 dbSNP
rs1014701584 565 dbSNP
rs983586749 566 dbSNP
rs1449686445 569 dbSNP
rs1170164340 572 dbSNP
rs1363336030 575 dbSNP
rs1456916573 578 dbSNP
rs1373626539 579 dbSNP
rs951781704 581 dbSNP
rs930810217 588 dbSNP
rs995895766 591 dbSNP
rs1364994320 598 dbSNP
rs1374549700 606 dbSNP
rs1191348398 607 dbSNP
rs115878264 612 dbSNP
rs62442791 613 dbSNP
rs1019031323 616 dbSNP
rs1258335809 622 dbSNP
rs577125373 622 dbSNP
rs1206811440 624 dbSNP
rs1008447941 626 dbSNP
rs991075956 626 dbSNP
rs1190079161 643 dbSNP
rs1190288348 644 dbSNP
rs1382952679 645 dbSNP
rs958640935 649 dbSNP
rs1164826033 656 dbSNP
rs1369743253 663 dbSNP
rs935512783 675 dbSNP
rs1319209746 679 dbSNP
rs1388549212 689 dbSNP
rs1436216912 691 dbSNP
rs746915085 699 dbSNP
rs904033557 704 dbSNP
rs1228015292 707 dbSNP
rs1034038495 726 dbSNP
rs565977432 729 dbSNP
rs1043807554 740 dbSNP
rs948138147 743 dbSNP
rs186721596 744 dbSNP
rs1329799334 748 dbSNP
rs1224804769 757 dbSNP
rs1306489768 762 dbSNP
rs992600591 764 dbSNP
rs557224671 765 dbSNP
rs939280230 773 dbSNP
rs1182141631 777 dbSNP
rs1257652878 780 dbSNP
rs1471284210 784 dbSNP
rs1157785112 792 dbSNP
rs1020004405 793 dbSNP
rs907821803 811 dbSNP
rs1161801868 825 dbSNP
rs1458268578 825 dbSNP
rs1416148902 826 dbSNP
rs1010110634 831 dbSNP
rs1447568052 833 dbSNP
rs1303577762 849 dbSNP
rs1381637277 853 dbSNP
rs1408022365 861 dbSNP
rs1287841861 862 dbSNP
rs1350997811 868 dbSNP
rs1230203867 880 dbSNP
rs1276224496 888 dbSNP
rs983236727 892 dbSNP
rs951853453 897 dbSNP
rs892965052 901 dbSNP
rs1257331083 903 dbSNP
rs1312237591 905 dbSNP
rs1027463434 908 dbSNP
rs1251974955 912 dbSNP
rs1473199066 930 dbSNP
rs974482030 940 dbSNP
rs1033371563 942 dbSNP
rs1423692465 946 dbSNP
rs996089644 955 dbSNP
rs900392792 956 dbSNP
rs1040387044 958 dbSNP
rs1177277461 959 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- 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' cgagacgagucuuGAUGUGAg 5'
                       :|||||| 
Target 5' -----auacuuuuUUACACUa 3'
1 - 16
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 GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000340881.2 | 3UTR | AUACUUUUUUACACUAAUUUUAUUG
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
67 hsa-miR-4280 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT065612 DAZAP2 DAZ associated protein 2 2 10
MIRT084985 BACH1 BTB domain and CNC homolog 1 2 2
MIRT088053 UBXN2A UBX domain protein 2A 2 4
MIRT097327 SCAMP1 secretory carrier membrane protein 1 2 2
MIRT099148 MYLIP myosin regulatory light chain interacting protein 2 12
MIRT127042 FAM208B family with sequence similarity 208 member B 2 4
MIRT140479 BNIP2 BCL2 interacting protein 2 2 6
MIRT154889 GNAS GNAS complex locus 2 4
MIRT187983 MBD6 methyl-CpG binding domain protein 6 2 2
MIRT190440 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT240673 GAPVD1 GTPase activating protein and VPS9 domains 1 2 2
MIRT295049 EVI5L ecotropic viral integration site 5 like 2 2
MIRT324749 ACER2 alkaline ceramidase 2 2 2
MIRT366075 FAM127A retrotransposon Gag like 8C 2 4
MIRT442625 LOX lysyl oxidase 2 2
MIRT445224 TYRP1 tyrosinase related protein 1 2 2
MIRT448967 CCNT2 cyclin T2 2 4
MIRT450137 PFN4 profilin family member 4 2 2
MIRT464350 USP46 ubiquitin specific peptidase 46 2 2
MIRT470460 PPP1R15B protein phosphatase 1 regulatory subunit 15B 2 2
MIRT473691 MAPK8 mitogen-activated protein kinase 8 2 4
MIRT480188 CALM2 calmodulin 2 2 6
MIRT486355 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 2 2
MIRT486708 TROVE2 TROVE domain family member 2 2 4
MIRT488337 SCD stearoyl-CoA desaturase 2 2
MIRT489322 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT491791 ZNF24 zinc finger protein 24 2 2
MIRT491970 USP37 ubiquitin specific peptidase 37 2 2
MIRT492029 TWF1 twinfilin actin binding protein 1 2 4
MIRT492063 TMEM245 transmembrane protein 245 2 2
MIRT492247 SLC39A9 solute carrier family 39 member 9 2 2
MIRT492254 SLC35F5 solute carrier family 35 member F5 2 2
MIRT492592 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT493436 KAT7 lysine acetyltransferase 7 2 2
MIRT493470 IPMK inositol polyphosphate multikinase 2 2
MIRT493639 HECTD1 HECT domain E3 ubiquitin protein ligase 1 2 2
MIRT493919 FAM127B retrotransposon Gag like 8A 2 4
MIRT494639 ARNTL aryl hydrocarbon receptor nuclear translocator like 2 2
MIRT500032 ABCF2 ATP binding cassette subfamily F member 2 2 8
MIRT504589 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide 2 4
MIRT505535 SP4 Sp4 transcription factor 2 6
MIRT507539 DNAJB6 DnaJ heat shock protein family (Hsp40) member B6 2 6
MIRT508846 TMCO1 transmembrane and coiled-coil domains 1 2 4
MIRT510488 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 2
MIRT511402 IFNAR2 interferon alpha and beta receptor subunit 2 2 6
MIRT523252 HIST1H2AH histone cluster 1 H2A family member h 2 2
MIRT525939 C11orf74 chromosome 11 open reading frame 74 2 2
MIRT531453 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 2 2
MIRT533317 UNKL unkempt family like zinc finger 2 2
MIRT541034 STRBP spermatid perinuclear RNA binding protein 2 8
MIRT546734 RNF217 ring finger protein 217 2 2
MIRT555125 PTPRJ protein tyrosine phosphatase, receptor type J 2 2
MIRT556105 MOAP1 modulator of apoptosis 1 2 2
MIRT560205 AK4 adenylate kinase 4 2 2
MIRT561087 LLPH LLP homolog, long-term synaptic facilitation 2 2
MIRT566967 LBR lamin B receptor 2 2
MIRT567344 H3F3B H3 histone family member 3B 2 2
MIRT567863 DCAF12 DDB1 and CUL4 associated factor 12 2 2
MIRT574449 SCML2 Scm polycomb group protein like 2 2 2
MIRT575700 Map1b microtubule-associated protein 1B 2 2
MIRT651432 YIPF6 Yip1 domain family member 6 2 2
MIRT659728 CCDC93 coiled-coil domain containing 93 2 2
MIRT686937 SFT2D3 SFT2 domain containing 3 2 2
MIRT699385 SLC30A6 solute carrier family 30 member 6 2 2
MIRT710287 CSNK1G3 casein kinase 1 gamma 3 2 2
MIRT715123 PANK3 pantothenate kinase 3 2 2
MIRT721847 VLDLR very low density lipoprotein receptor 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-4280 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4280 Platinum 23939 resistant tissue
hsa-miR-4280 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4280 Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-4280 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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