pre-miRNA Information | |
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pre-miRNA | hsa-mir-3675 |
Genomic Coordinates | chr1: 16858949 - 16859021 |
Description | Homo sapiens miR-3675 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3675-5p | |||||||||||||||||||||||||||||||||||||||||||||||||||
Sequence | 12| UAUGGGGCUUCUGUAGAGAUUUC |34 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | SYNDIG1L | ||||||||||||||||||||
Synonyms | CAPUCIN, DSPC1, IFITMD4, TMEM90A | ||||||||||||||||||||
Description | synapse differentiation inducing 1 like | ||||||||||||||||||||
Transcript | NM_001105579 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SYNDIG1L | |||||||||||||||||||||
3'UTR of SYNDIG1L (miRNA target sites are highlighted) |
>SYNDIG1L|NM_001105579|3'UTR 1 TAGCCAGTAGGGCCTGCATCCTGACTCCCCTGCCCACCTGAGGAAGCAGTGGGGCTTGGAGTTGCAGACCCTATGGAAAG 81 GCCCGGCCCCTGAAGATGATCCCGTGAGAGTGGCTTGCTGAGGGGGAGACCCCCATTCCACAGCCTGCAGAGCTCAGCCT 161 TCACTTCTGCTTGCCCGCTGCTCCCAGCCCCAGAGCAGGGCCCGGGGCGCCACTCTCTAACCCAGGCTACAGACGGGAAA 241 CAGAAGGCAGGGCTGCCCACCAGGCCATCCCAGCAGGGCCTAGCTCCATCCATTCTGCCCATTCCCTAGAGGATCTCCTG 321 CCCTACAGCCAGCCCACCACCTACCCTGCCAACCTCCCCACAGAGAAAGAGCAGGAGGTTACAGGGAGAAAAGGGGGTGC 401 CCAGAGCACAAGGGGACCCGTCCCAATCCTTTCAGCCCACAGGGATCTTCACCTGGGGACAGCCTGAGCTTCCCCCAACT 481 CCACTGTCTGGCCCCATCATGCCCAGACCTCAGCAGGCCAAGAAGGAAATACGTGGAGGCAAGGGGGCCTCTTGCTGTCT 561 CTGATTCTAGAGGGTGCTTATCTCTGCATGGGCTTGTGAGGCACTGTAGATTCTAGATAGGGAAGAGGAGCCTCGGTATG 641 TAAACTCTGAACCAAGGGCAGGTTCTTGGAGCTTCTTCATGCGGGTGCAAAAGGCAGTTGCAATGACAGAGAATAGAGGG 721 TCCTGAAATATTGCTGTACTACATGACTCTTCCTACTCTCCCCCCACTCCCCGCCCCTATCATCCTTTTCTGGGCTTTGC 801 CTGGGGGTCCGTGAGCTGGTGCCATCACAAGTAGACTAGACCCAGAGAGTGCCCTCAGCTCACCAGCCACTGAGCGCACG 881 GCCCTAGGTCCAGCCCTACAGAAAACGCAGCAAGGAGAGACCCTAGGGAGTAGTGAGTATAGATGAGGGAAGGGACTCAG 961 GGAAGGAATGGCCTGCTGAGTAGTCAGCGGTGCTTAGGAAGGCTTCCTGGAGGAGGTATCCCTTGAGCAAGTCCTAGGAT 1041 GAATAGAATTCATCTAAGGGATTTGGTCACATAACTCTTTGTATTTGTAGGCAGGGATGTGGCAGGAACCTTCCATGGGA 1121 AGCTTCCAGGCTGTTTGGATTCTGCCTGGAACATCTGGGCTGGAGCCAAACTACAGCCATTCCTAAGGGTTCTGCCAACT 1201 CAAGGAGGAACGTCACACCTGTCTCTCAAAGACCAATGATGTTTTCCCATCTCTGAATGCTAGGGGGTCAGTGGTGGGTA 1281 CCTGGTTACCCCTGGGGCATCTTCACTGATATCTCTGCTCAGTGCCAGTCTCAACACCCTCAGCCACTAGGGCACATCCA 1361 GAATTTTAGAGACATCTCCAGGTAGGCGGGGGGCAGCACCAATGTGGGCAGGCCTGTCTGGACTCAAGCTACAGGCCCCT 1441 GCTGTGCATGATGTGGGAACCTGGTCATTCCCATGCCCCATCCAGAGCCCAGGGCTGTGGCTCCACCACTGAGCATCCCT 1521 TGTCCCACTGTCCTCCCCTGCCTCGGGCACTGCCCAGCCCTCCACTCCTGCATCACAGCAGTTTTAAGGTCCCATTATTG 1601 TACTGATTTATCCTTGTAATAAATGTTTCTGTAACACCTGGTAAAAAAAAAAAAAAAAAAAAAA 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
... - 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 | ENST00000331628.3 | 3UTR | GUCAUUCCCAUGCCC |
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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32 hsa-miR-3675-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT366903 | NONO | non-POU domain containing octamer binding | ![]() |
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2 | 2 | ||||||
MIRT453894 | DUSP18 | dual specificity phosphatase 18 | ![]() |
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2 | 2 | ||||||
MIRT461725 | ZNF426 | zinc finger protein 426 | ![]() |
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2 | 2 | ||||||
MIRT464694 | UBE2V1 | ubiquitin conjugating enzyme E2 V1 | ![]() |
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2 | 2 | ||||||
MIRT465957 | TMEM189-UBE2V1 | TMEM189-UBE2V1 readthrough | ![]() |
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2 | 2 | ||||||
MIRT466038 | TMEM189 | transmembrane protein 189 | ![]() |
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2 | 2 | ||||||
MIRT471546 | PAX5 | paired box 5 | ![]() |
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2 | 2 | ||||||
MIRT472813 | MTMR12 | myotubularin related protein 12 | ![]() |
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2 | 2 | ||||||
MIRT474099 | LMBR1L | limb development membrane protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT480205 | CAD | carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase | ![]() |
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2 | 2 | ||||||
MIRT488268 | HSP90AB1 | heat shock protein 90 alpha family class B member 1 | ![]() |
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2 | 8 | ||||||
MIRT491222 | MRPL34 | mitochondrial ribosomal protein L34 | ![]() |
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2 | 2 | ||||||
MIRT494768 | AP1G1 | adaptor related protein complex 1 gamma 1 subunit | ![]() |
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2 | 2 | ||||||
MIRT497228 | MORC2 | MORC family CW-type zinc finger 2 | ![]() |
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2 | 2 | ||||||
MIRT501676 | PFN1 | profilin 1 | ![]() |
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2 | 6 | ||||||
MIRT511831 | H2AFX | H2A histone family member X | ![]() |
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2 | 4 | ||||||
MIRT513880 | HNRNPUL1 | heterogeneous nuclear ribonucleoprotein U like 1 | ![]() |
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2 | 4 | ||||||
MIRT519402 | DNASE2 | deoxyribonuclease 2, lysosomal | ![]() |
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2 | 4 | ||||||
MIRT522627 | MAP7D1 | MAP7 domain containing 1 | ![]() |
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2 | 4 | ||||||
MIRT546998 | PPP2CA | protein phosphatase 2 catalytic subunit alpha | ![]() |
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2 | 2 | ||||||
MIRT555119 | PUM2 | pumilio RNA binding family member 2 | ![]() |
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2 | 2 | ||||||
MIRT560380 | TIMM8A | translocase of inner mitochondrial membrane 8A | ![]() |
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2 | 2 | ||||||
MIRT572188 | CDADC1 | cytidine and dCMP deaminase domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT634822 | ASB6 | ankyrin repeat and SOCS box containing 6 | ![]() |
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2 | 2 | ||||||
MIRT641149 | DNMBP | dynamin binding protein | ![]() |
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2 | 2 | ||||||
MIRT647389 | ZNF616 | zinc finger protein 616 | ![]() |
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2 | 2 | ||||||
MIRT670851 | SFT2D2 | SFT2 domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT698600 | TEX261 | testis expressed 261 | ![]() |
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2 | 2 | ||||||
MIRT698691 | TBPL1 | TATA-box binding protein like 1 | ![]() |
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2 | 2 | ||||||
MIRT708725 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT718340 | SYNDIG1L | synapse differentiation inducing 1 like | ![]() |
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2 | 2 | ||||||
MIRT725514 | FBXO46 | F-box protein 46 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||
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