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 C11orf74   
Synonyms HEPIS, NWC
Description chromosome 11 open reading frame 74
Transcript NM_138787   
Expression
Putative miRNA Targets on C11orf74
3'UTR of C11orf74
(miRNA target sites are highlighted)
>C11orf74|NM_138787|3'UTR
   1 TTCACAGAGGCATTTTGTGTGTGTGTGCTTATTTTAATTTTGTTCTTATTCTAGCAACATTAGAATAAAAGATAAACCTA
  81 CTATAATTCCCTTTGTGGAAATTTAAAAAAAAAAAAAAAAAA
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' cgAGACGAGUCUUGAUGUGAg 5'
            |||  |:  |:| |||:| 
Target 5' gtTCTTATTCTAGCAACATTa 3'
42 - 62 107.00 -7.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM7652762 1 COSMIC
COSN30501389 3 COSMIC
COSN8338945 13 COSMIC
COSN30505030 28 COSMIC
COSN31524731 64 COSMIC
COSN31525806 72 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1476144424 1 dbSNP
rs373767699 2 dbSNP
rs1004056210 3 dbSNP
rs755174937 7 dbSNP
rs753979857 16 dbSNP
rs755280316 16 dbSNP
rs1403856783 20 dbSNP
rs1485603445 22 dbSNP
rs1320492393 23 dbSNP
rs781590307 24 dbSNP
rs1399422815 26 dbSNP
rs1276858241 27 dbSNP
rs1258989770 29 dbSNP
rs17549494 30 dbSNP
rs1335639274 32 dbSNP
rs1390275505 49 dbSNP
rs760750523 58 dbSNP
rs1015019760 59 dbSNP
rs148484429 65 dbSNP
rs961709893 77 dbSNP
rs973044928 78 dbSNP
rs1383642807 79 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 119710.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' cgagacgagucuugAUGUGAg 5'
                        ||||:| 
Target 5' --------------UACAUUu 3'
1 - 7
Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
CLIP-seq Support 1 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000534635.1 | 3UTR | UACAUUUUCUUUAUCCAUCCAUCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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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