pre-miRNA Information
pre-miRNA hsa-mir-3911   
Genomic Coordinates chr9: 127690687 - 127690795
Description Homo sapiens miR-3911 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3911
Sequence 12| UGUGUGGAUCCUGGAGGAGGCA |33
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
431152 7 ClinVar
COSM3847691 15 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs943029638 2 dbSNP
rs780635543 3 dbSNP
rs371437556 6 dbSNP
rs1135401819 7 dbSNP
rs748706130 14 dbSNP
rs1403241180 15 dbSNP
rs779344153 17 dbSNP
rs755366929 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SSX2B   
Synonyms CT5.2, CT5.2b, HOM-MEL-40, SSX
Description SSX family member 2B
Transcript NM_001164417   
Expression
Putative miRNA Targets on SSX2B
3'UTR of SSX2B
(miRNA target sites are highlighted)
>SSX2B|NM_001164417|3'UTR
   1 CTCCCCTCAGGGATACGACACATGCCCATGATGAGAAGCAGAACGTGGTGACCTTTCACGAACATGGGCATGGCTGCGGA
  81 CCCCTCGTCATCAGGTGCATAGCAAGTGAAAGCAAGTGTTCACAACAGTGAAAAGTTGAGCGTCATTTTTCTTAGTGTGC
 161 CAAGAGTTCGATGTTAGCGTTTACGTTGTATTTTCTTACACTGTGTCATTCTGTTAGATACTAACATTTTCATTGATGAG
 241 CAAGACATACTTAATGCATATTTTGGTTTGTGTATCCATGCACCTACCTTAGAAAACAAGTATTGTCGGTTACCTCTGCA
 321 TGGAACAGCATTACCCTCCTCTCTCCCCAGATGTGACTACTGAGGGCAGTTCTGAGTGTTTAATTTCAGATTTTTTCCTC
 401 TGCATTTACACACACACGCACACAAACCACACCACACACACACACACACACACACACACACACACACACACACACCAAGT
 481 ACCAGTATAAGCATCTGCCATCTGCTTTTCCCATTGCCATGCGTCCTGGTCAAGCTCCCCTCACTCTGTTTCCTGGTCAG
 561 CATGTACTCCCCTCATCCGATTCCCCTGTAGCAGTCACTGACAGTTAATAAACCTTTGCAAACGTTCAAAAAAAAAAAAA
 641 AAAAA
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' acGGAGGAGGUCCUAGGUGUGu 5'
            ::|||||: | ||::|||| 
Target 5' ttTTTCCTCT-GCATTTACACa 3'
392 - 412 135.00 -17.90
2
miRNA  3' acggaggagguccuaGGUGUGu 5'
                         |||||| 
Target 5' cgcacacaaaccacaCCACACa 3'
417 - 438 120.00 -14.10
3
miRNA  3' acggagGAGGUCCUAGGUGUGu 5'
                :|:  | |||||::| 
Target 5' ttttggTTTGTGTATCCATGCa 3'
261 - 282 116.00 -8.40
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1238564053 383 dbSNP
rs868953099 895 dbSNP
rs868975613 896 dbSNP
rs1307751840 897 dbSNP
rs868940166 897 dbSNP
rs1306864194 898 dbSNP
rs868952415 898 dbSNP
rs868940000 936 dbSNP
rs868959358 937 dbSNP
rs868928287 940 dbSNP
rs868935134 942 dbSNP
rs868993918 943 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acggaggagguccuaGGUGUGu 5'
                         |||||| 
Target 5' ------------acaCCACACa 3'
1 - 10
2
miRNA  3' acggaggagguccuagGUGUGu 5'
                          ||||| 
Target 5' cacacacacacacacaCACACa 3'
13 - 34
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BT474
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1395166. RNA binding protein: AGO. Condition:BT474 AGO HITS-CLIP Replicate 1 HITS-CLIP data was present in GSM1395167. RNA binding protein: AGO. Condition:BT474 AGO HITS-CLIP Replicate 2 ...

- Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al., 2014, Breast cancer research and treatment.

Article - Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al.
- Breast cancer research and treatment, 2014
miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.
LinkOut: [PMID: 24906430]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Cardiac Tissues
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM2202477. RNA binding protein: AGO2. Condition:S2_LV_25yo_Male_AGO2_bound_RNA HITS-CLIP data was present in GSM2202479. RNA binding protein: AGO2. Condition:S4_LV_29yo_Male_AGO2_bound_RNA HITS-CLIP data was present in GSM2202476. RNA binding protein: AGO2. Condition:S1_LV_54yo_Male_AGO2_bound_RNA HITS-CLIP data was present in GSM2202478. RNA binding protein: AGO2. Condition:S3_LV_36yo_Male_AGO2_bound_RNA ...

- Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research.

Article - Spengler RM; Zhang X; Cheng C; McLendon JM; et al.
- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
CLIP-seq Support 1 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000276049.6 | 3UTR | ACACCACACACACACACACACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1395166
Method / RBP HITS-CLIP / AGO
Cell line / Condition BT474 / BT474 AGO HITS-CLIP Replicate 1
Location of target site ENST00000276049.6 | 3UTR | CACCACACACACACACACACACACACACACACACACACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24906430 / GSE57855
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1395167
Method / RBP HITS-CLIP / AGO
Cell line / Condition BT474 / BT474 AGO HITS-CLIP Replicate 2
Location of target site ENST00000276049.6 | 3UTR | CACCACACACACACACACACACACACACACACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24906430 / GSE57855
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
70 hsa-miR-3911 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT207399 MAT2A methionine adenosyltransferase 2A 2 6
MIRT284537 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT291946 TPM4 tropomyosin 4 2 2
MIRT293609 PVR poliovirus receptor 2 2
MIRT357688 PAIP2 poly(A) binding protein interacting protein 2 2 2
MIRT451607 MEIS3P1 Meis homeobox 3 pseudogene 1 2 2
MIRT452110 IFITM1 interferon induced transmembrane protein 1 2 2
MIRT457804 KLHL25 kelch like family member 25 2 2
MIRT462730 EFNB1 ephrin B1 2 2
MIRT463219 ZNF131 zinc finger protein 131 2 2
MIRT464141 VPS28 VPS28, ESCRT-I subunit 2 2
MIRT467582 SLC7A5 solute carrier family 7 member 5 2 6
MIRT470824 PLXND1 plexin D1 2 2
MIRT474230 LCLAT1 lysocardiolipin acyltransferase 1 2 2
MIRT478989 COLGALT1 collagen beta(1-O)galactosyltransferase 1 2 2
MIRT479462 CDK6 cyclin dependent kinase 6 2 2
MIRT483558 SYT2 synaptotagmin 2 2 2
MIRT484483 SLC9A1 solute carrier family 9 member A1 2 2
MIRT485224 PRICKLE1 prickle planar cell polarity protein 1 2 2
MIRT490356 DPYSL5 dihydropyrimidinase like 5 2 4
MIRT493177 MKNK2 MAP kinase interacting serine/threonine kinase 2 2 2
MIRT509802 CHAF1B chromatin assembly factor 1 subunit B 2 4
MIRT511815 HDGF heparin binding growth factor 2 2
MIRT512254 ARPP19 cAMP regulated phosphoprotein 19 2 6
MIRT513025 GPT2 glutamic--pyruvic transaminase 2 2 2
MIRT519640 ZNF772 zinc finger protein 772 2 4
MIRT531178 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 2 2
MIRT537870 EDA2R ectodysplasin A2 receptor 2 2
MIRT551914 IGLON5 IgLON family member 5 2 2
MIRT558359 DMTF1 cyclin D binding myb like transcription factor 1 2 2
MIRT559771 URGCP-MRPS24 URGCP-MRPS24 readthrough 2 4
MIRT559813 ZNF83 zinc finger protein 83 2 2
MIRT561999 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT565754 SERTAD2 SERTA domain containing 2 2 2
MIRT569423 DCAF8 DDB1 and CUL4 associated factor 8 2 2
MIRT569845 RGS5 regulator of G protein signaling 5 2 2
MIRT606928 CDK15 cyclin dependent kinase 15 2 2
MIRT607616 TMEM130 transmembrane protein 130 2 4
MIRT607629 TRIOBP TRIO and F-actin binding protein 2 2
MIRT607885 SATB1 SATB homeobox 1 2 2
MIRT607942 SSX2 SSX family member 2 2 4
MIRT608017 CARNS1 carnosine synthase 1 2 4
MIRT608036 UBLCP1 ubiquitin like domain containing CTD phosphatase 1 2 2
MIRT608063 SSX2B SSX family member 2B 2 4
MIRT608558 SBK1 SH3 domain binding kinase 1 2 6
MIRT608915 NCDN neurochondrin 2 6
MIRT615876 HIF1AN hypoxia inducible factor 1 alpha subunit inhibitor 2 4
MIRT618023 ELFN1 extracellular leucine rich repeat and fibronectin type III domain containing 1 2 2
MIRT620505 SNRPD1 small nuclear ribonucleoprotein D1 polypeptide 2 2
MIRT628101 IL1RAPL1 interleukin 1 receptor accessory protein like 1 2 2
MIRT628700 ZNF548 zinc finger protein 548 2 2
MIRT630658 POU2F1 POU class 2 homeobox 1 2 2
MIRT643508 ZNF28 zinc finger protein 28 2 2
MIRT646379 SLC22A6 solute carrier family 22 member 6 2 2
MIRT660041 C15orf61 chromosome 15 open reading frame 61 2 2
MIRT687700 KRR1 KRR1, small subunit processome component homolog 2 2
MIRT688858 CAMKK2 calcium/calmodulin dependent protein kinase kinase 2 2 2
MIRT690443 REPIN1 replication initiator 1 2 2
MIRT690456 ZNF33A zinc finger protein 33A 2 2
MIRT693796 RHOG ras homolog family member G 2 2
MIRT694274 ZNF529 zinc finger protein 529 2 4
MIRT697697 WAC WW domain containing adaptor with coiled-coil 2 2
MIRT700242 RCC2 regulator of chromosome condensation 2 2 2
MIRT701836 MRPL37 mitochondrial ribosomal protein L37 2 2
MIRT704255 DHCR24 24-dehydrocholesterol reductase 2 2
MIRT707203 SDK2 sidekick cell adhesion molecule 2 2 2
MIRT710365 CREB5 cAMP responsive element binding protein 5 2 2
MIRT711943 WDFY1 WD repeat and FYVE domain containing 1 2 2
MIRT715496 MAZ MYC associated zinc finger protein 2 2
MIRT719250 MS4A1 membrane spanning 4-domains A1 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-3911 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3911 Ceritinib 57379345 NSC776422 approved resistant High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-3911 Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-3911 Dabrafenib 44462760 NSC764134 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-3911 Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-3911 Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-mir-3911 Vincristine 5978 approved resistant cell line (W1)
hsa-mir-3911 Androstenedione+Letrozole sensitive cell line (MCF-7)
hsa-miR-3911 Palbociclib 5330286 NSC758247 approved resistant tissue (breast cancer)
hsa-miR-3911 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3911 Doxorubicin 31703 NSC123127 approved sensitive cell line (HS578T)
hsa-miR-3911 Tamoxifen+Fulvestrant sensitive cell line (LCC9)
hsa-miR-3911 Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-3911 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3911 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-3911 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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