pre-miRNA Information | |
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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 | |||||||||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-516b-3p | ||||||||||||||||||||||||||||||||||||||||||
Sequence | 56| UGCUUCCUUUCAGAGGGU |73 | ||||||||||||||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||||||||||||||
Experiments | Array-cloned | ||||||||||||||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | PCTP | ||||||||||||||||||||
Synonyms | PC-TP, STARD2 | ||||||||||||||||||||
Description | phosphatidylcholine transfer protein | ||||||||||||||||||||
Transcript | NM_001102402 | ||||||||||||||||||||
Other Transcripts | NM_021213 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PCTP | |||||||||||||||||||||
3'UTR of PCTP (miRNA target sites are highlighted) |
>PCTP|NM_001102402|3'UTR 1 GAAAGAGAACTGGGAACATTGCATCCATGGGTTGATGTCTCTGGAAGTGCAACCACCCAATGTCTCTGGAAGTGCCACCT 81 GGAAGTGCCACCTGGAAGTGTCTCTGGAAGAGCACCCACCACTGTTCAGCCTTCCCCTGCTGTTTCTGTCTTCAGAGGCC 161 TACACACTACCACATCCTTTCTAAGCATGTTTGCCTGACATCCAGCTCACTCGTCTGCTTCCTTTCTCGCTCCCCCCATC 241 CTGGGCTGGGCTGCCTTCTTCTACAGTTCAATATGGGGCAGACTAGGGAAACCTTTGCTTGCTTACTATTAGGAGGGGAA 321 GTCTTCAGTAGGGAACACGATCATTCCATTGTGCAATTTTACGGGGATGGGTGGGCGGAGGGACACAACAAAATTTAAGA 401 ATGACTATTTGGGCGGGCTGGCTCTTTTGCAGCTTGTGATTTCTTCCAGCTTGGGAGGGGCTGCTGGAAGTGGCATTTCG 481 TTCAGAGCTGACTTTCAGTGCACCCAAACTGGATGACGTGCCAATGTCCATTTGCCTTATGCTTTGTGGAGCTGATTAGG 561 CTGGGATTTGAGGTGATAATCCAGTAAGTCTTTCCTCGTTCCTACTTGTGGAGGATCAGTAGCTGTTATGATGCCAGACC 641 ATTTGGAGAAGTATCAGAGGCCTGACCGGACACATAATATGACAACCACATTTTTCCTCATCATCCATGAGGAAATGGAT 721 GATTTCTCTTTTCCATATGTCACTGGGGGAAAGGCTGCCTGTACCTCTCAAGCTTTGCATTTTACTGGAAACTGAGGCGT 801 CAAGATGGCTGTGGCAGCTAGCAAAAGCAAAGATGCTTTGTGCATAGCCTTGTGAAAAAGTATCTTTCTATGCAATAAGA 881 TGAATTTTCCTCCCAGAATATTTAGAAATGTAGAAGGGATAACAGTTCACAGCCAGGTAAAATTTAACTGGTGGCTTAAT 961 GACTCTGCACCTTTTTCTCAGGAATTCTGCCTAAGTTGTCTGCCTTTTCTACCACCAAAAAGACTTTTAGTTTTCTATGC 1041 TTTCTCCTGAATTTTGGTAGGGTAAGGTATTTCTATGTCAAAGGCACAGCCTTGATGATCTCAGGGAAAAATTTTAATCA 1121 CTGTGTATAATGATACTGAACCTTGATTAATAACAGAAATTCAGGATGTAAAGCCACAGAATGGGATTTATTAATGTGGG 1201 ATACCTCAGACTGTTTGTTTTCTTTCTGGGAAGAAAAGTGTGTTCTATAATGAATAAATATAGAGTGGTTTTTACTTGTC 1281 CTGTGTAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HeLa | ||||||
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 Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B
HITS-CLIP data was present in Chi_ControlA_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control A
... - Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Chi SW; Zang JB; Mele A; Darnell RB - Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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CLIP-seq Support 1 for dataset Chi_124B_2A8_130_50 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HeLa / HeLa cell miR-124 + B |
Location of target site | ENST00000576183.1 | 3UTR | UAAGGAAGCCAUGCAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset Chi_ControlA_2A8_130_50 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HeLa / HeLa cell Control A |
Location of target site | ENST00000576183.1 | 3UTR | UAAGGAAGCCAUGCAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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85 hsa-miR-516b-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT077049 | SMARCE1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 | ![]() |
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2 | 2 | ||||||
MIRT155261 | IFNAR2 | interferon alpha and beta receptor subunit 2 | ![]() |
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2 | 4 | ||||||
MIRT446119 | ASTN1 | astrotactin 1 | ![]() |
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2 | 2 | ||||||
MIRT447355 | STOM | stomatin | ![]() |
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2 | 2 | ||||||
MIRT469329 | RGP1 | RGP1 homolog, RAB6A GEF complex partner 1 | ![]() |
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2 | 2 | ||||||
MIRT470201 | PSAT1 | phosphoserine aminotransferase 1 | ![]() |
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2 | 6 | ||||||
MIRT475944 | GXYLT1 | glucoside xylosyltransferase 1 | ![]() |
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2 | 4 | ||||||
MIRT498268 | KIAA1644 | KIAA1644 | ![]() |
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2 | 2 | ||||||
MIRT501725 | OVOL1 | ovo like transcriptional repressor 1 | ![]() |
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2 | 2 | ||||||
MIRT522860 | KIAA1551 | KIAA1551 | ![]() |
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2 | 2 | ||||||
MIRT527900 | B3GALT5 | beta-1,3-galactosyltransferase 5 | ![]() |
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2 | 4 | ||||||
MIRT528557 | DNAAF3 | dynein axonemal assembly factor 3 | ![]() |
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2 | 2 | ||||||
MIRT531250 | peptide deformylase, mitochondrial | ![]() |
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2 | 2 | |||||||
MIRT534410 | SENP1 | SUMO1/sentrin specific peptidase 1 | ![]() |
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2 | 2 | ||||||
MIRT544656 | MED19 | mediator complex subunit 19 | ![]() |
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2 | 2 | ||||||
MIRT550681 | YARS | tyrosyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT557208 | HNRNPF | heterogeneous nuclear ribonucleoprotein F | ![]() |
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2 | 4 | ||||||
MIRT611532 | DDB1 | damage specific DNA binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT612087 | TIMM10 | translocase of inner mitochondrial membrane 10 | ![]() |
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2 | 2 | ||||||
MIRT616535 | PARD6B | par-6 family cell polarity regulator beta | ![]() |
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2 | 4 | ||||||
MIRT616738 | DCTN5 | dynactin subunit 5 | ![]() |
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2 | 2 | ||||||
MIRT616754 | SVOP | SV2 related protein | ![]() |
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2 | 4 | ||||||
MIRT617380 | FAM227A | family with sequence similarity 227 member A | ![]() |
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2 | 2 | ||||||
MIRT617624 | RAB3IP | RAB3A interacting protein | ![]() |
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2 | 2 | ||||||
MIRT620778 | MT1A | metallothionein 1A | ![]() |
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2 | 2 | ||||||
MIRT623172 | NAA50 | N(alpha)-acetyltransferase 50, NatE catalytic subunit | ![]() |
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2 | 2 | ||||||
MIRT626034 | AREL1 | apoptosis resistant E3 ubiquitin protein ligase 1 | ![]() |
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2 | 2 | ||||||
MIRT627376 | PRICKLE4 | prickle planar cell polarity protein 4 | ![]() |
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2 | 2 | ||||||
MIRT630533 | AGO3 | argonaute 3, RISC catalytic component | ![]() |
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2 | 2 | ||||||
MIRT631686 | NQO2 | N-ribosyldihydronicotinamide:quinone reductase 2 | ![]() |
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2 | 2 | ||||||
MIRT633896 | FGF10 | fibroblast growth factor 10 | ![]() |
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2 | 2 | ||||||
MIRT635933 | PLA2G12A | phospholipase A2 group XIIA | ![]() |
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2 | 2 | ||||||
MIRT636275 | RFFL | ring finger and FYVE like domain containing E3 ubiquitin protein ligase | ![]() |
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2 | 2 | ||||||
MIRT636285 | RAD51L3-RFFL | RAD51L3-RFFL readthrough | ![]() |
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2 | 2 | ||||||
MIRT636502 | GDAP1L1 | ganglioside induced differentiation associated protein 1 like 1 | ![]() |
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2 | 2 | ||||||
MIRT638037 | SHPK | sedoheptulokinase | ![]() |
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2 | 2 | ||||||
MIRT639162 | LAMTOR3 | late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 | ![]() |
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2 | 2 | ||||||
MIRT639571 | GORASP1 | golgi reassembly stacking protein 1 | ![]() |
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2 | 2 | ||||||
MIRT641248 | CENPN | centromere protein N | ![]() |
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2 | 2 | ||||||
MIRT643650 | MYOCD | myocardin | ![]() |
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2 | 2 | ||||||
MIRT645490 | TRIM63 | tripartite motif containing 63 | ![]() |
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2 | 2 | ||||||
MIRT648016 | SLCO4C1 | solute carrier organic anion transporter family member 4C1 | ![]() |
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2 | 2 | ||||||
MIRT648102 | LRRFIP1 | LRR binding FLII interacting protein 1 | ![]() |
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2 | 2 | ||||||
MIRT648729 | HIST1H2BD | histone cluster 1 H2B family member d | ![]() |
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2 | 2 | ||||||
MIRT650177 | LILRA2 | leukocyte immunoglobulin like receptor A2 | ![]() |
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2 | 2 | ||||||
MIRT652787 | TCEANC2 | transcription elongation factor A N-terminal and central domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT653248 | SORD | sorbitol dehydrogenase | ![]() |
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2 | 2 | ||||||
MIRT654859 | PPM1F | protein phosphatase, Mg2+/Mn2+ dependent 1F | ![]() |
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2 | 2 | ||||||
MIRT655533 | PAG1 | phosphoprotein membrane anchor with glycosphingolipid microdomains 1 | ![]() |
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2 | 2 | ||||||
MIRT656390 | MCU | mitochondrial calcium uniporter | ![]() |
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2 | 2 | ||||||
MIRT656881 | KIF1C | kinesin family member 1C | ![]() |
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2 | 2 | ||||||
MIRT657083 | JMY | junction mediating and regulatory protein, p53 cofactor | ![]() |
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2 | 2 | ||||||
MIRT657629 | GPX8 | glutathione peroxidase 8 (putative) | ![]() |
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2 | 2 | ||||||
MIRT658295 | FAM83F | family with sequence similarity 83 member F | ![]() |
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2 | 2 | ||||||
MIRT659432 | COL1A1 | collagen type I alpha 1 chain | ![]() |
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2 | 2 | ||||||
MIRT659791 | CBLB | Cbl proto-oncogene B | ![]() |
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2 | 2 | ||||||
MIRT660153 | BRCC3 | BRCA1/BRCA2-containing complex subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT660490 | ARRDC3 | arrestin domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT660503 | ARPC2 | actin related protein 2/3 complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT666356 | SIKE1 | suppressor of IKBKE 1 | ![]() |
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2 | 2 | ||||||
MIRT677774 | FKTN | fukutin | ![]() |
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2 | 2 | ||||||
MIRT688556 | DCAF16 | DDB1 and CUL4 associated factor 16 | ![]() |
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2 | 2 | ||||||
MIRT697415 | ZFP91 | ZFP91 zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT709468 | KRTAP19-1 | keratin associated protein 19-1 | ![]() |
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2 | 2 | ||||||
MIRT711154 | WDR82P1 | WD repeat domain 82 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT711467 | SRD5A1 | steroid 5 alpha-reductase 1 | ![]() |
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2 | 2 | ||||||
MIRT712515 | ENPP5 | ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative) | ![]() |
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2 | 2 | ||||||
MIRT712661 | PCTP | phosphatidylcholine transfer protein | ![]() |
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2 | 2 | ||||||
MIRT713304 | TYRP1 | tyrosinase related protein 1 | ![]() |
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2 | 2 | ||||||
MIRT714597 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT716603 | MPPED1 | metallophosphoesterase domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT717537 | PYGO2 | pygopus family PHD finger 2 | ![]() |
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2 | 2 | ||||||
MIRT718058 | CYP3A5 | cytochrome P450 family 3 subfamily A member 5 | ![]() |
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2 | 2 | ||||||
MIRT718539 | PIGQ | phosphatidylinositol glycan anchor biosynthesis class Q | ![]() |
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2 | 2 | ||||||
MIRT719768 | ZNF236 | zinc finger protein 236 | ![]() |
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2 | 2 | ||||||
MIRT720162 | PNPO | pyridoxamine 5'-phosphate oxidase | ![]() |
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2 | 2 | ||||||
MIRT720360 | ZBTB8B | zinc finger and BTB domain containing 8B | ![]() |
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2 | 2 | ||||||
MIRT721182 | HOPX | HOP homeobox | ![]() |
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2 | 2 | ||||||
MIRT721278 | RAD54L2 | RAD54 like 2 | ![]() |
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2 | 2 | ||||||
MIRT721357 | ENTHD1 | ENTH domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT721504 | CARHSP1 | calcium regulated heat stable protein 1 | ![]() |
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2 | 2 | ||||||
MIRT721918 | LINGO2 | leucine rich repeat and Ig domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT722278 | LURAP1 | leucine rich adaptor protein 1 | ![]() |
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2 | 2 | ||||||
MIRT722789 | FUT4 | fucosyltransferase 4 | ![]() |
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2 | 2 | ||||||
MIRT724390 | ABAT | 4-aminobutyrate aminotransferase | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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