miRTarBase - #MIRT612087


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pre-miRNA Information
pre-miRNA hsa-mir-516b-1   
Genomic Coordinates chr19: 53736845 - 53736934
Synonyms MIRN516-4, MIRN516B-1, MIRN516B1, MIR516B1
Description Homo sapiens miR-516b-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-516b-2   
Genomic Coordinates chr19: 53725442 - 53725526
Synonyms MIRN516-3, MIRN516B-2, MIRN516B2, MIR516B2
Description Homo sapiens miR-516b-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-516b-3p
Sequence 56| UGCUUCCUUUCAGAGGGU |73
Evidence Experimental
Experiments Array-cloned
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1413434631 1 dbSNP
rs746170707 2 dbSNP
rs1312744198 2 dbSNP
rs752101959 3 dbSNP
rs770077784 4 dbSNP
rs1193425541 6 dbSNP
rs953142850 7 dbSNP
rs1020245150 7 dbSNP
rs775845942 11 dbSNP
rs1402471980 11 dbSNP
rs760158839 15 dbSNP
rs78861479 16 dbSNP
rs765933705 16 dbSNP
Putative Targets

Gene Information
Gene Symbol TIMM10   
Synonyms TIM10, TIM10A, TIMM10A
Description translocase of inner mitochondrial membrane 10
Transcript NM_012456   
Expression
Putative miRNA Targets on TIMM10
3'UTR of TIMM10
(miRNA target sites are highlighted)		 
>TIMM10|NM_012456|3'UTR
   1 GGTCCCTGTCAGTATACACCCTGGGGTGTACCCCACCCCTTCCCACTTTAATAAACGTGCTCCCTGTTGGGTGTCATCTG
  81 TGAAGACTGCCAGGCCTAGGCTCTCTGTAGAGAGTCTTCAAGATCCCGGAGTGGTAGCGCTGTCTCCTGGTGAAGGAGTA
 161 TTTGTCACACTGGAATGTGACTGTGTGTGTATGTATGTGTATATATATATATATATATATATATATATATATAAACAAGT
 241 TTGTTGACACCTACAAAAAAAAAA
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' ugGGAGAC--UUUCCUUcgu 5'
            |: |||  :|||||:   
Target 5' gtCTCCTGGTGAAGGAGtat 3'
 142 - 161 98.00 -11.90
2 
miRNA  3' ugGGAGACUUUCCUUCGu 5'
            :| | ||: || ||| 
Target 5' gaTCCCGGAGTGGTAGCg 3'
 122 - 139 92.00 -13.50
3 
miRNA  3' ugGGAGACUUUCCUUCGu 5'
            :|||||  || :||: 
Target 5' gcTCTCTG-TAGAGAGTc 3'
 100 - 116 91.00 -13.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30526156 44 COSMIC
COSN31553665 56 COSMIC
COSN30154618 107 COSMIC
COSN23706353 139 COSMIC
COSN31590596 144 COSMIC
COSN31582330 160 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs776762079 1 dbSNP
rs1486574813 5 dbSNP
rs768543618 14 dbSNP
rs746888576 16 dbSNP
rs1457967124 19 dbSNP
rs775562451 25 dbSNP
rs1449435142 29 dbSNP
rs1158697299 31 dbSNP
rs527550516 37 dbSNP
rs1195812793 38 dbSNP
rs745894555 39 dbSNP
rs751754790 40 dbSNP
rs1260908069 44 dbSNP
rs932364653 56 dbSNP
rs946221479 57 dbSNP
rs1308535025 60 dbSNP
rs924943249 62 dbSNP
rs1212895245 64 dbSNP
rs147027025 67 dbSNP
rs1279324115 75 dbSNP
rs1221992923 77 dbSNP
rs1264600800 85 dbSNP
rs1198455195 119 dbSNP
rs1197410615 127 dbSNP
rs1054646791 128 dbSNP
rs764989240 138 dbSNP
rs1237906460 139 dbSNP
rs113266452 142 dbSNP
rs1409989744 156 dbSNP
rs945302524 160 dbSNP
rs913791914 163 dbSNP
rs1349601850 168 dbSNP
rs1417160413 170 dbSNP
rs1376659252 177 dbSNP
rs1456844904 177 dbSNP
rs991971121 182 dbSNP
rs1198220078 191 dbSNP
rs1300413627 191 dbSNP
rs1334103042 192 dbSNP
rs1408665880 195 dbSNP
rs1286116793 199 dbSNP
rs1357012729 199 dbSNP
rs1311744357 201 dbSNP
rs867732608 201 dbSNP
rs926754405 203 dbSNP
rs1387622979 205 dbSNP
rs377270733 205 dbSNP
rs372263572 207 dbSNP
rs1249650142 208 dbSNP
rs1472407819 209 dbSNP
rs1409844039 211 dbSNP
rs1190224075 213 dbSNP
rs1422422683 216 dbSNP
rs1173225511 220 dbSNP
rs1391295108 221 dbSNP
rs952116538 224 dbSNP
rs1256637833 226 dbSNP
rs1376684269 228 dbSNP
rs1044771614 229 dbSNP
rs1207976559 230 dbSNP
rs1376764137 231 dbSNP
rs545177663 232 dbSNP
rs1298008845 233 dbSNP
rs1448468633 233 dbSNP
rs10547275 234 dbSNP
rs1167254171 234 dbSNP
rs1211159767 234 dbSNP
rs1226009219 234 dbSNP
rs1236476969 234 dbSNP
rs1237099720 234 dbSNP
rs1272576950 234 dbSNP
rs1295539771 234 dbSNP
rs1314019920 234 dbSNP
rs1320993233 234 dbSNP
rs1341393483 234 dbSNP
rs1449413104 234 dbSNP
rs369115194 234 dbSNP
rs58460878 234 dbSNP
rs71470272 234 dbSNP
rs777885201 234 dbSNP
rs1207574994 236 dbSNP
rs1364107953 236 dbSNP
rs1048156468 238 dbSNP
rs1284753451 244 dbSNP
rs1305522434 247 dbSNP
rs917677797 248 dbSNP
rs1027661525 250 dbSNP
rs1219858339 254 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 GSM1084083. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SigmaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ugggagaCUUUCCUUCgu 5'
                 ||:|| |||  
Target 5' cagugagGAGAGAAAGgg 3'
 		2 - 19
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]
CLIP-seq Support 1 for dataset GSM1084083
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_SigmaAb
Location of target site ENST00000257245.4 | 3UTR | CCAGUGAGGAGAGAAAGGGGACGAUGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
GSE27834 Pluripotent stem cells 0.352 9.1e-2 0.282 1.4e-1 16 Click to see details
GSE21849 B cell lymphoma -0.242 1.0e-1 -0.169 1.9e-1 29 Click to see details
GSE32688 Pancreatic cancer 0.153 2.0e-1 -0.087 3.2e-1 32 Click to see details
GSE17306 Multiple myeloma 0.088 2.7e-1 0.352 6.6e-3 49 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.017 4.7e-1 0.029 4.5e-1 25 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
85 hsa-miR-516b-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT077049 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 2 2
MIRT155261 IFNAR2 interferon alpha and beta receptor subunit 2 2 4
MIRT446119 ASTN1 astrotactin 1 2 2
MIRT447355 STOM stomatin 2 2
MIRT469329 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT470201 PSAT1 phosphoserine aminotransferase 1 2 6
MIRT475944 GXYLT1 glucoside xylosyltransferase 1 2 4
MIRT498268 KIAA1644 KIAA1644 2 2
MIRT501725 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT522860 KIAA1551 KIAA1551 2 2
MIRT527900 B3GALT5 beta-1,3-galactosyltransferase 5 2 4
MIRT528557 DNAAF3 dynein axonemal assembly factor 3 2 2
MIRT531250 PDF peptide deformylase, mitochondrial 2 2
MIRT534410 SENP1 SUMO1/sentrin specific peptidase 1 2 2
MIRT544656 MED19 mediator complex subunit 19 2 2
MIRT550681 YARS tyrosyl-tRNA synthetase 2 2
MIRT557208 HNRNPF heterogeneous nuclear ribonucleoprotein F 2 4
MIRT611532 DDB1 damage specific DNA binding protein 1 2 2
MIRT612087 TIMM10 translocase of inner mitochondrial membrane 10 2 2
MIRT616535 PARD6B par-6 family cell polarity regulator beta 2 4
MIRT616738 DCTN5 dynactin subunit 5 2 2
MIRT616754 SVOP SV2 related protein 2 4
MIRT617380 FAM227A family with sequence similarity 227 member A 2 2
MIRT617624 RAB3IP RAB3A interacting protein 2 2
MIRT620778 MT1A metallothionein 1A 2 2
MIRT623172 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 2 2
MIRT626034 AREL1 apoptosis resistant E3 ubiquitin protein ligase 1 2 2
MIRT627376 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT630533 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT631686 NQO2 N-ribosyldihydronicotinamide:quinone reductase 2 2 2
MIRT633896 FGF10 fibroblast growth factor 10 2 2
MIRT635933 PLA2G12A phospholipase A2 group XIIA 2 2
MIRT636275 RFFL ring finger and FYVE like domain containing E3 ubiquitin protein ligase 2 2
MIRT636285 RAD51L3-RFFL RAD51L3-RFFL readthrough 2 2
MIRT636502 GDAP1L1 ganglioside induced differentiation associated protein 1 like 1 2 2
MIRT638037 SHPK sedoheptulokinase 2 2
MIRT639162 LAMTOR3 late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 2 2
MIRT639571 GORASP1 golgi reassembly stacking protein 1 2 2
MIRT641248 CENPN centromere protein N 2 2
MIRT643650 MYOCD myocardin 2 2
MIRT645490 TRIM63 tripartite motif containing 63 2 2
MIRT648016 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT648102 LRRFIP1 LRR binding FLII interacting protein 1 2 2
MIRT648729 HIST1H2BD histone cluster 1 H2B family member d 2 2
MIRT650177 LILRA2 leukocyte immunoglobulin like receptor A2 2 2
MIRT652787 TCEANC2 transcription elongation factor A N-terminal and central domain containing 2 2 2
MIRT653248 SORD sorbitol dehydrogenase 2 2
MIRT654859 PPM1F protein phosphatase, Mg2+/Mn2+ dependent 1F 2 2
MIRT655533 PAG1 phosphoprotein membrane anchor with glycosphingolipid microdomains 1 2 2
MIRT656390 MCU mitochondrial calcium uniporter 2 2
MIRT656881 KIF1C kinesin family member 1C 2 2
MIRT657083 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT657629 GPX8 glutathione peroxidase 8 (putative) 2 2
MIRT658295 FAM83F family with sequence similarity 83 member F 2 2
MIRT659432 COL1A1 collagen type I alpha 1 chain 2 2
MIRT659791 CBLB Cbl proto-oncogene B 2 2
MIRT660153 BRCC3 BRCA1/BRCA2-containing complex subunit 3 2 2
MIRT660490 ARRDC3 arrestin domain containing 3 2 2
MIRT660503 ARPC2 actin related protein 2/3 complex subunit 2 2 2
MIRT666356 SIKE1 suppressor of IKBKE 1 2 2
MIRT677774 FKTN fukutin 2 2
MIRT688556 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT697415 ZFP91 ZFP91 zinc finger protein 2 2
MIRT709468 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT711154 WDR82P1 WD repeat domain 82 pseudogene 1 2 2
MIRT711467 SRD5A1 steroid 5 alpha-reductase 1 2 2
MIRT712515 ENPP5 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative) 2 2
MIRT712661 PCTP phosphatidylcholine transfer protein 2 2
MIRT713304 TYRP1 tyrosinase related protein 1 2 2
MIRT714597 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT716603 MPPED1 metallophosphoesterase domain containing 1 2 2
MIRT717537 PYGO2 pygopus family PHD finger 2 2 2
MIRT718058 CYP3A5 cytochrome P450 family 3 subfamily A member 5 2 2
MIRT718539 PIGQ phosphatidylinositol glycan anchor biosynthesis class Q 2 2
MIRT719768 ZNF236 zinc finger protein 236 2 2
MIRT720162 PNPO pyridoxamine 5'-phosphate oxidase 2 2
MIRT720360 ZBTB8B zinc finger and BTB domain containing 8B 2 2
MIRT721182 HOPX HOP homeobox 2 2
MIRT721278 RAD54L2 RAD54 like 2 2 2
MIRT721357 ENTHD1 ENTH domain containing 1 2 2
MIRT721504 CARHSP1 calcium regulated heat stable protein 1 2 2
MIRT721918 LINGO2 leucine rich repeat and Ig domain containing 2 2 2
MIRT722278 LURAP1 leucine rich adaptor protein 1 2 2
MIRT722789 FUT4 fucosyltransferase 4 2 2
MIRT724390 ABAT 4-aminobutyrate aminotransferase 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-516b Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-516b Bromocriptine approved 31101 Microarray Prolactinoma 22366961 2012 up-regulated
miR-516b Bromocriptine approved 31101 Quantitative real-time PCR Prolactinoma 22366961 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-516b-3p Paclitaxel 36314 NSC125973 approved sensitive High Pan-Cancer cell line (NCI-H460, NCI-H522, NCI-H322M, HOP62, A549, EKVX, MALME-3M, NCI-H226, HT-29, HCT-116, SE-620, HCT-15, HCC2998, COLO205, HS-578T, NCI/ADR-RES, OVCAR8, OVCAR4, ACHN, SN-12C, 786-O, CAKI-1, UO-31, TK-10, A498, SK-MEL-28, UACC-257, M14, UACC-62, SK
hsa-miR-516b-3p Ribavirin+Pegylated IFNa-2b sensitive tissue (chronic hepatitis C)
hsa-miR-516b-3p Testosterone+Exemestane sensitive cell line (MCF-7)
hsa-miR-516b-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (MGC-803)
hsa-miR-516b-3p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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