pre-miRNA Information | |
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pre-miRNA | hsa-mir-3152 |
Genomic Coordinates | chr9: 18573306 - 18573379 |
Description | Homo sapiens miR-3152 stem-loop |
Comment | Berezikov et al. proposed this sequence as a miRNA candidate based on the RAKE method . |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3152-3p | |||||||||||||||||||||||||||||||||
Sequence | 45| UGUGUUAGAAUAGGGGCAAUAA |66 | |||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||
Experiments | Illumina | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TBRG1 | ||||||||||||||||||||
Synonyms | NIAM, TB-5 | ||||||||||||||||||||
Description | transforming growth factor beta regulator 1 | ||||||||||||||||||||
Transcript | NM_032811 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TBRG1 | |||||||||||||||||||||
3'UTR of TBRG1 (miRNA target sites are highlighted) |
>TBRG1|NM_032811|3'UTR 1 ACAAGAAGGGATCAGATGCCACATCGTTTTTGTCGTGATTAATTTAACTTAAACTAAAATTTTGGGTATATGAAAGAAGG 81 CAGCAATTCAGAAGTAAAGAAGATACTAACGTATTTCATCATGGAAGGTCCTGTGGTGATGGTTTTCCCTGGGAAAACCT 161 TCAGCTGCTTTATTTTTAGTAATAAATTTCTCTTGTCAATTCTGTTTACTTTCATCTTGTAATCGGGATGTAATCTTTTT 241 TGCTTAGCTCTGCCTGAGGTAAAGTAAACTTCAGCCTCTTATAAACAAGAGTGATAGAGAGCTGCAGGCTGCTACAACAA 321 ATACCATAGACAGGTTGGTTTATAAATAACATGAATTTATTTCTCACAGTTCTGGATGCTGGGAAGTCCAAGTTCAAGGA 401 GCGCAGATTCAATGTCTGGTGAGGGCCCACTTCCTAGTTCTTAGACAGCTGTCTTCCTGCAGTGTCCTCACGTGGTAGAA 481 GAGGAAGGCAGCTCTCCGGGGTCCCTTTTATAAGATCACTAAGCCGGTTCATGAGAGGTCTGCTCTCATGACCTAATCAC 561 CTCCCAAAGGCCCCACCTCCCAATACCATCACATTAGGGGTTAGGATTTAACATGAATTTTGGGGACATATAAACATTAA 641 GTCTGTAGTAGCAGCAGCTGACTAACGAGGGAGATAGGGAGATTCTGACAAACTTCTACTCTTGATTGTGATCCTAATTC 721 AAGGAATATCAAGTCCCAGCCCCTGCAACCCAGGCTGCTGCTTAATTTTCATGTCAGTATCATCAAAATCCAATGTTCTG 801 CTTAAACTCAAGATGGAAAGTCCAGTCCAAGGTACACTGTTCATCTTTTTCTTCACATTTTGCACATCCTTCAAGGGGAT 881 CTTTAACCTCTTTAACCTTTGTATTGCACCTCAGATAATGTGCTTTTTAGCTCAGTACACTGAAACCATATGATAACACA 961 AATTCACATATAATTGGGGGTTAGTCCCATACTCTATAACAGACTTAGTCCTGTCTTTTCATTAGCCATGTAATAATATA 1041 ACTCCATGTTCCATGCAACTGGATTTTTGGACCCTGTTAATAGCATTAAGGTAGAGGTTTACTCTATCACCTAACACCTC 1121 AACACTACCTGTGGGATGCCTTAGTTACCCAGCAGCAGGTTACCAAGGGCTGTCTGGAAAGGGAGGGACAAAAGGACCCA 1201 GAAGTAGAAGAATGGGGATGGAGTGGTGAGAATTGAATGGTTAATGCACTGCCATTCATAATTGCCAATTGAGGACAACA 1281 CAAATGGGATTGGTACTTTATAGTAATAAATCTGACCAGCAGAGGGAGGGATCAGGCAGCAGTGTTTAGAGCACACCACA 1361 CTGGCCACTGTAAACTGAGAAGCTAAGTTAACTGGTATTTTATGATTTTGAGTATAGTCTTTTTATAAGTTGTATACACT 1441 TTACAATGTAAAAGAAACAAACTTTGTATAATAGCAAATCGGGAAGGGGACTGCTTAAAATGTTAATGCAGTGTTTTTCT 1521 TTTTTTCTCTGCATAAATGGCTTGAGCATACTGGCATTTACACAGAAATGATATATGCTGCTTTTATCATATAACAAATA 1601 TTTTCCCACTATTACAGCCTGAGTAATACCCGTATTAAAAGAGCCTCATTTTAGAAAGACATTTAAAATTTTTGGAACAT 1681 ACCACATGTAGAAAGGTTGAACTGGTTTTTCAGCTATAATGCATATACAACTATAGTGTGTACGTATACCACATATACAT 1761 ATACTTGTATGAAGATATGTGTAAAATGTTTTTACTATGGATCATGGATTTAAGAAACTTGAAAAGCTGGGCACGGTGGC 1841 TCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCAAGAGGTCAGGAGATCGAGACCATCCTGGCTAAG 1921 TCGGTCTCTAATAAAAATACAAAAAATTAGCCAGGCGTGGTGGCACGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGG 2001 CAGGAAGAATCGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCGAGACCGCGCCACTGCACTCCAGCCTGGGCAACAG 2081 AGCAAAACTCCAACTCAAAAACAAAAACAAAAACACCTTGAAAAACACTGCCTTAGTATACTTAAACTATCTTTTCATCT 2161 ATCAGATTGTTAAGGATTTTTTTTAAATTTGACAACATCCAGTGTCAATGAGGGTGAGGGCAAAAAAAGGACTACCTTGG 2241 TGAGAATGTAAGTTGTTTAATCCTTTGGGAGGGTTAAGCTGTAGATATCTAAATTTTAAATATATATTTATCCTCTTCCA 2321 TGTTAAGAACCCTAAGAAATAACTGGACGAGTGTGGTATGATGTTTGCATGTGATATTCATTACAGTATTATTTTAATAG 2401 TAGAAAATTGTTAAAAATCTATATGTCCATTAATAGGAAATTGGTTAAATAAAATGAGGCTTCCACAAACTGAAACACTC 2481 TAAATCTATATTCTATTATTTACATAAGAAAATTATTTTGGTAAAGTAAGTAAGTCAAAAACACAGATTACAAAATAATA 2561 TGTACTGTATAAAATTATATAACTCAAGTCAAGTGAATGGTTCAGCAAAATAGTGTTTCTCTGAATGATGAATTTGGGGG 2641 TGATTTTTACTTGCTTATACTTTAGTGTCCAAATTTTCTACAGTGACTATAAATTTCATTTTAAAACTAAAAAGTTCTTA 2721 CATTTGGGGAAATGCAGTGAATTCCCACATCATGTTTTAAATTACTCAGCCACTAAAAATGAATGTGCATGGCGTCATTA 2801 ACATAATCATTGCCTGAACCGTATTTTTCACACTATGTACTCTAGGTTCCTGGAGGTGAAAGGAATCTGGACTTAGAGTT 2881 CTTGGCTACCTCTGGCTGCCCCCGAATTAGAACAGCCCATGGGGGTATGTGTATTGGGAGTGGAGGAGTGGACGGGTAGA 2961 TTGACTTTTTCTCAGGCATCAATCTGTTACAAGGTTCATGGTTTCTATGGGGCCAGATGCATGAGAGGTCAAAGCATGGG 3041 CAATAGGGGTTAACTGAACGAGTTGAATGCTAGGAAGTCCTCAGGGGAGCCAACGTTCCTTGTAAAGTGTGTAGATTTTT 3121 TGTTTTTTAACTAAATAAAATCTTGGCACTGACAAAGTTATTCCTGCTGTTTGGAGCTACACCAGAACCCCTTGGAACTC 3201 TACAGAGGGGTAGAACTAAAGCAAAAACCATCATTCACCCTACAGAGTATTATAAATTTCATTTTCACACAGTAAAAAGT 3281 TCCTAAATTGGGGGAAACATAGTGAATTCCACATAATGTTTTAAATTATTCAGCCACTAAAAATAAATTTACATATGATT 3361 TCATTAATATATTCACTATCTAAACCATATTTTTTACACTACGTAAAATACATTGTATATGTACAGTGAGTGATGCTTTT 3441 TGCTTTAGTTCTCATTTTTCACATTAAGGGGAGGAAAGCTACCCATAGATAGTATTCTTACTCCTTTTCACATGCTTCAA 3521 GGACAGTTTGCAAGTGGATATAAATACATACACATCACTAGTGATTATGCTTTTATTTATTTCCAACTTCTTATAGGTAA 3601 CATAATTTTCAGACAATGTTAGCTGTTTTTAATCCATCAGTAAACTGCATTAAGATTCTTAATAAACAAACACTGAAGGC 3681 CTCTTTCA 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 | C8166 | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
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CLIP-seq Support 1 for dataset GSM4903833 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
Location of target site | NM_032811 | 3UTR | GAAACCAUAUGAUAACACAAAUUCACAUAUAAUUGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903835 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_032811 | 3UTR | AGCUCAGUACACUGAAACCAUAUGAUAACACAAAUUCACAUAUAAUUGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903837 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_032811 | 3UTR | UGCUUUUUAGCUCAGUACACUGAAACCAUAUGAUAACACAAAUUCACAUAUAAUUGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000441174.3 | 3UTR | UUUACUCUAUCACCUAACACCUCAACACUACCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||
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60 hsa-miR-3152-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT068760 | RB1 | RB transcriptional corepressor 1 | 2 | 2 | ||||||||
MIRT142268 | DCTN5 | dynactin subunit 5 | 2 | 8 | ||||||||
MIRT179443 | TBRG1 | transforming growth factor beta regulator 1 | 2 | 2 | ||||||||
MIRT221382 | DNAJB6 | DnaJ heat shock protein family (Hsp40) member B6 | 2 | 6 | ||||||||
MIRT332510 | CD81 | CD81 molecule | 2 | 2 | ||||||||
MIRT442419 | KCNN3 | potassium calcium-activated channel subfamily N member 3 | 2 | 2 | ||||||||
MIRT445519 | PLXDC2 | plexin domain containing 2 | 2 | 2 | ||||||||
MIRT464185 | VMA21 | VMA21, vacuolar ATPase assembly factor | 2 | 2 | ||||||||
MIRT467933 | SLC16A6 | solute carrier family 16 member 6 | 2 | 2 | ||||||||
MIRT468378 | SETD5 | SET domain containing 5 | 2 | 2 | ||||||||
MIRT468486 | SESN3 | sestrin 3 | 2 | 2 | ||||||||
MIRT468928 | RPS24 | ribosomal protein S24 | 2 | 2 | ||||||||
MIRT478171 | DENND5B | DENN domain containing 5B | 2 | 2 | ||||||||
MIRT490447 | GLUD1 | glutamate dehydrogenase 1 | 2 | 2 | ||||||||
MIRT494675 | ARL5B | ADP ribosylation factor like GTPase 5B | 2 | 2 | ||||||||
MIRT502287 | GNG5 | G protein subunit gamma 5 | 2 | 6 | ||||||||
MIRT506078 | PPP2CA | protein phosphatase 2 catalytic subunit alpha | 2 | 6 | ||||||||
MIRT508008 | BCAT1 | branched chain amino acid transaminase 1 | 2 | 4 | ||||||||
MIRT508760 | IPP | intracisternal A particle-promoted polypeptide | 2 | 2 | ||||||||
MIRT509091 | SYNPO2L | synaptopodin 2 like | 2 | 4 | ||||||||
MIRT511968 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | 2 | 4 | ||||||||
MIRT515210 | CRCP | CGRP receptor component | 2 | 2 | ||||||||
MIRT516377 | TRAF3IP2 | TRAF3 interacting protein 2 | 2 | 4 | ||||||||
MIRT517047 | ZNF678 | zinc finger protein 678 | 2 | 2 | ||||||||
MIRT521125 | SHROOM4 | shroom family member 4 | 2 | 2 | ||||||||
MIRT521277 | RTF1 | RTF1 homolog, Paf1/RNA polymerase II complex component | 2 | 2 | ||||||||
MIRT522772 | LAMP2 | lysosomal associated membrane protein 2 | 2 | 6 | ||||||||
MIRT524419 | CNKSR3 | CNKSR family member 3 | 2 | 2 | ||||||||
MIRT529398 | ICK | intestinal cell kinase | 2 | 2 | ||||||||
MIRT529965 | PHF7 | PHD finger protein 7 | 2 | 2 | ||||||||
MIRT530189 | TIGD2 | tigger transposable element derived 2 | 2 | 2 | ||||||||
MIRT533716 | TMEM30A | transmembrane protein 30A | 2 | 2 | ||||||||
MIRT543170 | FICD | FIC domain containing | 2 | 2 | ||||||||
MIRT548496 | E2F8 | E2F transcription factor 8 | 2 | 2 | ||||||||
MIRT555020 | RAB23 | RAB23, member RAS oncogene family | 2 | 2 | ||||||||
MIRT560728 | ZNF529 | zinc finger protein 529 | 2 | 10 | ||||||||
MIRT564890 | YTHDF3 | YTH N6-methyladenosine RNA binding protein 3 | 2 | 2 | ||||||||
MIRT567327 | HMGB1 | high mobility group box 1 | 2 | 2 | ||||||||
MIRT568035 | CLIP4 | CAP-Gly domain containing linker protein family member 4 | 2 | 2 | ||||||||
MIRT574763 | FLVCR1 | feline leukemia virus subgroup C cellular receptor 1 | 2 | 2 | ||||||||
MIRT620811 | SLC26A2 | solute carrier family 26 member 2 | 2 | 2 | ||||||||
MIRT622456 | RNF19B | ring finger protein 19B | 2 | 2 | ||||||||
MIRT636240 | SIM1 | single-minded family bHLH transcription factor 1 | 2 | 2 | ||||||||
MIRT643231 | MUC15 | mucin 15, cell surface associated | 2 | 2 | ||||||||
MIRT646319 | CAPZA2 | capping actin protein of muscle Z-line alpha subunit 2 | 2 | 2 | ||||||||
MIRT646674 | CCDC69 | coiled-coil domain containing 69 | 2 | 2 | ||||||||
MIRT650043 | VHL | von Hippel-Lindau tumor suppressor | 2 | 2 | ||||||||
MIRT652533 | TM9SF3 | transmembrane 9 superfamily member 3 | 2 | 2 | ||||||||
MIRT663022 | CD40LG | CD40 ligand | 2 | 2 | ||||||||
MIRT667465 | MAPK10 | mitogen-activated protein kinase 10 | 2 | 2 | ||||||||
MIRT668620 | EEA1 | early endosome antigen 1 | 2 | 2 | ||||||||
MIRT675678 | SLC35F5 | solute carrier family 35 member F5 | 2 | 2 | ||||||||
MIRT681814 | N4BP2L2 | NEDD4 binding protein 2 like 2 | 2 | 2 | ||||||||
MIRT682674 | CPM | carboxypeptidase M | 2 | 2 | ||||||||
MIRT701447 | NFIC | nuclear factor I C | 2 | 2 | ||||||||
MIRT706222 | C20orf144 | chromosome 20 open reading frame 144 | 2 | 2 | ||||||||
MIRT707510 | PPP1R16B | protein phosphatase 1 regulatory subunit 16B | 2 | 2 | ||||||||
MIRT710466 | ASTN2 | astrotactin 2 | 2 | 2 | ||||||||
MIRT712957 | SGCD | sarcoglycan delta | 2 | 2 | ||||||||
MIRT723030 | MYLIP | myosin regulatory light chain interacting protein | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||
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