pre-miRNA Information | |
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pre-miRNA | hsa-mir-6839 |
Genomic Coordinates | chr7: 64679064 - 64679176 |
Description | Homo sapiens miR-6839 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-6839-3p | ||||||||||||
Sequence | 92| UUGGGUUUUCUCUUCAAUCCAG |113 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | Meta-analysis | DRVs in miRNA |
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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 | SYNGAP1 | ||||||||||||||||||||
Synonyms | MRD5, RASA1, RASA5, SYNGAP | ||||||||||||||||||||
Description | synaptic Ras GTPase activating protein 1 | ||||||||||||||||||||
Transcript | NM_006772 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SYNGAP1 | |||||||||||||||||||||
3'UTR of SYNGAP1 (miRNA target sites are highlighted) |
>SYNGAP1|NM_006772|3'UTR 1 CCCACCCAGCATCAGAGACCTTCTCTTCCTTTCCTGTGCACCCCACCCTGTAACAGCACCAACCACCAGGATTGGACATC 81 ACCGAGGAACAGCGGGATTGCCTCCCCGAATGCCTCCCTGGGAGGCACACTGATTGCCCACCCCCACCACTGCACCATTT 161 CCAGGAGGGAGAGTGGGGACCCTCAGCCGCCCCCTTTTCCTTCCCATTGGGGTGCTGCCCTCTCTTTGACCCCCAGGGAC 241 CCTTGCCCCAGGACACCGCCTACCCCGTACAGACCCCTTCACTCCGGGGTGCTATCCCCATCCTCTGCCTCATCGTTCCC 321 CTGAGCACTGGGGGACAGACCCTCACCCCCACCCTGGGGGTGTGGCACCTCCAAACTTTCAACTTCAGGGTGATTTTTTT 401 AGCAGTAACCAGAGCTGACAATCTAACTCCCCTCCACCGCCCCATTTTGGCCTCCCCTGCCCCCCTTGTTATGGGGAGGG 481 GACCCCGGGTGAGGGGGCCCTATTACCCCTTGATTTCTCAGGAGCGTCTGGGGGGGCTCAGCACGCACAAACTCCTTCTC 561 CTTCTACCACTCTTAAATTTACTCCCTCCCCACCCAGAACCCAGATGGGGTGGAGGGGGCCACCGGGGCAGGGAGGGGGC 641 GGCAAGGGGGGAATGGGAGTTGTCTCCCCTTCTCCCCACACCTGATCTGCTCTCGGCTGGTCCCAGAGCGGGGTGAGGGG 721 GCTTATGCCCCCCCCTCCCCCAGTGTGTTGGGTGGGGTGGAATTGAGGTTAGGGTGAGGGGTCAGGGTTTAGGAGGGTGT 801 GTATGTTGGGAGGACAGGCTAGTTGATCTGTCCTACTCTGACACACAGTCCCCTCTGCCCCTTCCTTCTCTCTTCTTGGT 881 CTCTACTCCCAGGGGGAGGGGGGAACTTACTCTAGGAAAAGCCATGTCTCTCTCCCCCAGGGTGGGGGGACCTGTGTTGG 961 AGGAGGGGTGTTGGGGGGCCCCCTTCCATGACTCTGTCCCCTGGGGGAGGTAGGACAGGGCTGGGCTTCCCTCTCATCCT 1041 CCCCCTCCCAATCTCCTTCCACCTCCCTCCCTCCCGCCAGCTCCACGATTTTTCGGTGTTTCTCTGTACATAGTTTTCTG 1121 GCGGGATAGGGGAGGTAGGATGGATGGGGTTTGGGGTGGGTAGGCCATGGGAGGGGAGAAGCCCCTCCTTGGCACCCCCT 1201 CTTCCCTGACTGCTGTCCCCTACCCAGCCTTGCCCCCTTCATCCTTTTGCGTTTGGTATTGAGACTCTCCTAGACTCTAC 1281 TCCTCTTTCTTTTGTATGGACAGTTCCCCTTCAGTCCCATCCCCCTACACATACACCCAGCCGGGGCCAAATTTATACTT 1361 ATATAAAAGTTGTAAATATGTGAAATTTTATCCCTGTGCCCTTTCCCCACCTCAGGCCCTACCCCTGGACCCTCCCCAAC 1441 CTTCCTTCTCTCTTCTTTGGCTGTTGTAATTATCTGGGGTTTGTACTGTACATATCCGGGGTGTGTGTGTGTGGGCTGGG 1521 GGCAACCCTTCTGTACAGAGCTTCCTGGCCCCCTCCCCCCCCGCCCCTCTGCTTCCCTCCCCACCCACCACCTCAAGGGT 1601 AGGGAGTTGCTCTTCCTACCTGTTTTATTTTGTTTTCTCGTTCTCCCTCCCCACCCCACTCCCAGCCTTATCTATCCCCC 1681 CTCACTGTCCCCTTTTCTCCACTCCCAGCCCCATTTCCTTTTTTTCTGGAGTGTGTGGTGAAACAGAAAAAAACATGTTT 1761 AATAAACGGAGATTGTTCTTTTAA 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_124A_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + 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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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HEK293S |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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HITS-CLIP data was present in GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb
HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb
HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb
HITS-CLIP data was present in GSM1084083. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_SigmaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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]
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CLIP-seq Support 1 for dataset Chi_124A_2A8_130_50 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HeLa / HeLa cell miR-124 + A |
Location of target site | ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAACC |
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 GSM1084064 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_AbnovaAb |
Location of target site | ENST00000456692.2 | 3UTR | GAAUGAGAAAAAAAAAAAAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM1084065 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_AbnovaAb |
Location of target site | ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAACC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1084069 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SigmaAb |
Location of target site | ENST00000456692.2 | 3UTR | AAUGAGAAAAAAAAAAAACC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM1084083 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_hippuristanol_rep2_SigmaAb |
Location of target site | ENST00000456692.2 | 3UTR | AUGAGAAAAAAAAAAAAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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62 hsa-miR-6839-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT059162 | TXNIP | thioredoxin interacting protein | ![]() |
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2 | 2 | ||||||
MIRT064872 | ZBTB18 | zinc finger and BTB domain containing 18 | ![]() |
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2 | 2 | ||||||
MIRT065802 | HOXC8 | homeobox C8 | ![]() |
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2 | 4 | ||||||
MIRT106005 | SDCBP | syndecan binding protein | ![]() |
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2 | 2 | ||||||
MIRT275773 | TFDP1 | transcription factor Dp-1 | ![]() |
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2 | 2 | ||||||
MIRT314032 | PAPD7 | poly(A) RNA polymerase D7, non-canonical | ![]() |
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2 | 2 | ||||||
MIRT360277 | HIST1H2BE | histone cluster 1 H2B family member e | ![]() |
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2 | 8 | ||||||
MIRT360301 | HIST1H2BH | histone cluster 1 H2B family member h | ![]() |
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2 | 2 | ||||||
MIRT450086 | OR2A4 | olfactory receptor family 2 subfamily A member 4 | ![]() |
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2 | 2 | ||||||
MIRT468815 | RSRC2 | arginine and serine rich coiled-coil 2 | ![]() |
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2 | 6 | ||||||
MIRT475093 | IRF2BP2 | interferon regulatory factor 2 binding protein 2 | ![]() |
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2 | 4 | ||||||
MIRT477575 | EIF1AD | eukaryotic translation initiation factor 1A domain containing | ![]() |
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2 | 2 | ||||||
MIRT483926 | LCORL | ligand dependent nuclear receptor corepressor like | ![]() |
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2 | 6 | ||||||
MIRT504381 | HIST1H1C | histone cluster 1 H1 family member c | ![]() |
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2 | 4 | ||||||
MIRT506970 | HNRNPUL1 | heterogeneous nuclear ribonucleoprotein U like 1 | ![]() |
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2 | 6 | ||||||
MIRT507028 | HIST1H3B | histone cluster 1 H3 family member b | ![]() |
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2 | 6 | ||||||
MIRT511561 | HIST3H2BB | histone cluster 3 H2B family member b | ![]() |
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2 | 4 | ||||||
MIRT511650 | HIST1H3D | histone cluster 1 H3 family member d | ![]() |
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2 | 6 | ||||||
MIRT511696 | HIST1H2BL | histone cluster 1 H2B family member l | ![]() |
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2 | 4 | ||||||
MIRT511737 | HIST1H2BB | histone cluster 1 H2B family member b | ![]() |
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2 | 6 | ||||||
MIRT511746 | HIST1H2BA | histone cluster 1 H2B family member a | ![]() |
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2 | 8 | ||||||
MIRT515260 | CSNK1E | casein kinase 1 epsilon | ![]() |
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2 | 2 | ||||||
MIRT516220 | RAB3B | RAB3B, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT523281 | HIST1H1E | histone cluster 1 H1 family member e | ![]() |
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2 | 2 | ||||||
MIRT524121 | DMXL1 | Dmx like 1 | ![]() |
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2 | 2 | ||||||
MIRT530744 | GPR82 | G protein-coupled receptor 82 | ![]() |
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2 | 2 | ||||||
MIRT532214 | CCDC117 | coiled-coil domain containing 117 | ![]() |
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2 | 2 | ||||||
MIRT546182 | TPRG1L | tumor protein p63 regulated 1 like | ![]() |
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2 | 2 | ||||||
MIRT558638 | CNNM2 | cyclin and CBS domain divalent metal cation transport mediator 2 | ![]() |
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2 | 2 | ||||||
MIRT559562 | ARF1 | ADP ribosylation factor 1 | ![]() |
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2 | 4 | ||||||
MIRT560680 | HIST1H1T | histone cluster 1 H1 family member t | ![]() |
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2 | 2 | ||||||
MIRT570746 | AAK1 | AP2 associated kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT609518 | RAB3IP | RAB3A interacting protein | ![]() |
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2 | 2 | ||||||
MIRT612583 | SYNGAP1 | synaptic Ras GTPase activating protein 1 | ![]() |
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2 | 4 | ||||||
MIRT615733 | RIOK3 | RIO kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT616068 | SIX1 | SIX homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT617903 | SGCD | sarcoglycan delta | ![]() |
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2 | 2 | ||||||
MIRT620851 | SERPING1 | serpin family G member 1 | ![]() |
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2 | 2 | ||||||
MIRT625107 | SLC1A5 | solute carrier family 1 member 5 | ![]() |
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2 | 2 | ||||||
MIRT625120 | NUP93 | nucleoporin 93 | ![]() |
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2 | 2 | ||||||
MIRT625893 | LINC00632 | long intergenic non-protein coding RNA 632 | ![]() |
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2 | 2 | ||||||
MIRT626569 | MED7 | mediator complex subunit 7 | ![]() |
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2 | 2 | ||||||
MIRT626694 | ZFP14 | ZFP14 zinc finger protein | ![]() |
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2 | 4 | ||||||
MIRT626808 | PRR11 | proline rich 11 | ![]() |
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2 | 2 | ||||||
MIRT628131 | HM13 | histocompatibility minor 13 | ![]() |
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2 | 2 | ||||||
MIRT636596 | DCAF5 | DDB1 and CUL4 associated factor 5 | ![]() |
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2 | 2 | ||||||
MIRT649866 | SLFN12L | schlafen family member 12 like | ![]() |
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2 | 2 | ||||||
MIRT652133 | TRPM7 | transient receptor potential cation channel subfamily M member 7 | ![]() |
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2 | 2 | ||||||
MIRT652663 | TIMELESS | timeless circadian clock | ![]() |
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2 | 2 | ||||||
MIRT658335 | FAM83D | family with sequence similarity 83 member D | ![]() |
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2 | 2 | ||||||
MIRT660615 | ANKS4B | ankyrin repeat and sterile alpha motif domain containing 4B | ![]() |
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2 | 2 | ||||||
MIRT666304 | SLC22A3 | solute carrier family 22 member 3 | ![]() |
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2 | 2 | ||||||
MIRT668528 | ERGIC2 | ERGIC and golgi 2 | ![]() |
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2 | 2 | ||||||
MIRT692510 | PARD3 | par-3 family cell polarity regulator | ![]() |
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2 | 2 | ||||||
MIRT694784 | DHFRL1 | dihydrofolate reductase 2 | ![]() |
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2 | 2 | ||||||
MIRT700510 | PTPN14 | protein tyrosine phosphatase, non-receptor type 14 | ![]() |
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2 | 2 | ||||||
MIRT701438 | NFYA | nuclear transcription factor Y subunit alpha | ![]() |
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2 | 2 | ||||||
MIRT710155 | MTRF1L | mitochondrial translational release factor 1 like | ![]() |
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2 | 2 | ||||||
MIRT711436 | DLC1 | DLC1 Rho GTPase activating protein | ![]() |
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2 | 2 | ||||||
MIRT716979 | GPR155 | G protein-coupled receptor 155 | ![]() |
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2 | 2 | ||||||
MIRT720155 | POU2F2 | POU class 2 homeobox 2 | ![]() |
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2 | 2 | ||||||
MIRT722512 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 |