pre-miRNA Information | |
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pre-miRNA | hsa-mir-1245b |
Genomic Coordinates | chr2: 188978093 - 188978161 |
Description | Homo sapiens miR-1245b stem-loop |
Comment | None |
RNA Secondary Structure | |
Associated Diseases |
Mature miRNA Information | |||||||||||||||||||
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Mature miRNA | hsa-miR-1245b-3p | ||||||||||||||||||
Sequence | 42| UCAGAUGAUCUAAAGGCCUAUA |63 | ||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | SLC48A1 | ||||||||||||||||||||
Synonyms | HRG-1, HRG1, hHRG-1 | ||||||||||||||||||||
Description | solute carrier family 48 member 1 | ||||||||||||||||||||
Transcript | NM_017842 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SLC48A1 | |||||||||||||||||||||
3'UTR of SLC48A1 (miRNA target sites are highlighted) |
>SLC48A1|NM_017842|3'UTR 1 CCCAGGGGGTGAGGTCTCTGCACCCTGGGGGGGCCTTAGGACCTGGACTCAGCCTCTGAGATGTTGGGAGAGGCTACTCC 81 CACCCCCTGGTGACCCCAGAACTGTGGCAGAAAATACACAGCAGGACGAGTGTGGTCTCCCAGGAAGCTGTCCTGCCCGT 161 CCCCTTTCGAGGAAACCTGAGTGTGGTAGAGAGGGGATCCTGCCATGTTGCTCCTCATCAGCCTGGCCAGAGGGCAGCTT 241 TAGACCTTTTCAAATGAATCTGTTTTCTTTTCTTTCTTTTTTTTTTCTTTTTTTTTTTTTTTTGAGATGGAGTCTTACTC 321 TGTCACCCAGGCTGGAGTGCAGTAGTGCGATCTCAGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCAATTCTCCTGCC 401 TTGGCCTCTCAAGTAGCTGGGATTACAGGCATCTGCCACCATGCCCGGCAAATTTTTGTGTTTTTAGTAGAGACAGGGTT 481 TTGCCATGTTGGCCAGGCTGGTCTCGAACTCCTGATCTCAGGTGATTCACCCGCCTCAGCCTTCCAAAGTGCTGGGATTA 561 TAGGTGTGAGCCACCGTGCCCGGCCTGGATCTGTTTTCTTAGCACGCAGTGAGGAATCTTTGTACTTAAGGCCAGGGCAA 641 CAAAGTCAAGAGGTCAAGGTGTAGGGCCATGAGGCCTGGACCTATGCTGCAGGCAAGGGTTTCCATCCCCGCTGCCCTAG 721 GCACTCTCTTCCCAAGGCCAGGTTGGGCACCTGGGGAGGTCAGTTCAGAAATATCTAGCAGAGACCTCTTAAACCCCCAT 801 CCCAGCACCCCATCCTGTTGTTCCCAGAGCTGGTCTCCCATGAGTGTGCTAGAGCCAGATAGCCGTGGCCCCCCACCCAT 881 CTCACTCACACACACAGGCATCCATACACCCCAGAAGACTTCCCAAATGAGGCCAGACTCAGGGTCACGGGGAATGTGCT 961 TCTGCCCCTGTAAGGGCTTTGGGGAAGGGGGCAACATAGTAGAGGCTGGAAAGAGCCCCCAAACCTGTACCCATGCCCCT 1041 CCAGCCCTGCGTTTCCATTCTGCCTTCTCAGAGTGCCCTTGCTGCACCCAGACCACCGGCCAGGAGAGACCTTCTCTCCC 1121 ACTCCAGCCCCTCTCACTGCCCTTCAACTAGAGCTTTCACCTTTTTACATTTCCCTTCTGAAGGACACAAATCTGCTTTT 1201 CTGCCCATACACTGGCCCAAGGGCTCACCTAACTTGGGAGGGAAGGGGCTGTTGGTACAAGGATGATTTTCTGTTAGACT 1281 GCCATTTTGCACGGTCTCCCCCTTCCCATCTGATGTGTCCTGCCCCTCAGCTCTTTGCCTTATCTGTGTCACTGTCACTT 1361 TAGCAAAAATACAGCGGCCATTTGTATCAGCCTCTGGTGGTTGCTTGTGAGGTGGGACTCTTGCGGGAACAGGTGGACTT 1441 TGGGAGGAGTGGGCAGGGAGGGAGTGGTAGTGGCAGTTCTCGAGCTATCTGATTAAGCCATTCCGCTAGTTCAGTTGTGC 1521 CCTGGAGGGCAGGGGACAGAGTCAGTATCTCTGGGGCTGCAGGCCCTCTTGCCTTGGCCCTCCTGGCATGGGGTAACCAC 1601 CAGCTCAGCTCTCCTCCTCCAGCTTTCCTCTCTCTAGCACACCCCAGCCAGGGCAAGGATGCCCACGGGCATAGCTACAG 1681 CAACCCCTGCGGGATTTGGTGTCCACACCCGAGAGGCCAGGCCAGATGGGAAAGGGATTAGCGCCTCTTCCCTCACACTC 1761 TGCCAGGCTGCCAGGAGCTTGGGCCAGGTCTAAGGTAATGAGGTGCTCCTCTTCCTGCTGGAAAAACCGGACAGACTCAG 1841 AACCACAAAGGCAGGTGCTGCCAGCCTGGCGCCTTCCTCTCTGCTTAGGCTGGGTGAGCTTGTCCAGGCCTGTGCCTCAC 1921 CCCTTCTCTCTTCTAGGCTCAGTGTATGCTTAATCAGGCATGGTGCATCAGAGCGGGAAGGAGCCATCAACAGTGTATAC 2001 TTCTGGAGCCTTCTACTGATAAACAGAGGCCCCAGAAGACGATTTGACTTACCTGAGCTCCCAGCTGGGACTTAAACCCA 2081 GGTGTGTCTGAGTCACAACTCTTCGGGGATGCCGTGGTGAGCTGGGGCTGAGCTCCTGTATTCCCACTCCCCCACCCCAC 2161 CCCCACTCCTGCCATATCAGGGCTGGTCTCTGTGGACTCAGCCCAGGGCTGCCTCCTCTTTGTCACCCCAAAGTGGGGCA 2241 GCCAGGGACAGCCAGGGTGTGTTCAGAATGGGTTCTTCCTGCAGGGCAGGAAGGGCAGATTGTTAAAGGGGCTGCGGCCC 2321 AGACCACCCTGGTCCCTCCTCCGGCAGTGACTCAGACCCACACTGTGCCGTGCAGCTGTGTGCCCTGCACACCCGCTTGA 2401 CGGCGCACTGCTCACTTCTGGGGGGCCCTTTCAGAGGCACTTTTAAAGCAAATAAAACATTTATTGTTCAGA 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. |
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_017842 | 3UTR | UUUUCUGCCCAUACACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903834 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_b |
Location of target site | NM_017842 | 3UTR | UGCCCAUACACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 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_017842 | 3UTR | CACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_017842 | 3UTR | CCAUACACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 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_017842 | 3UTR | ACACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM4903838 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_017842 | 3UTR | CUGCCCAUACACUGGCCCAAGGGCUCACCUAACUUGGGAGGGAAGGGGCUGUUGGUACAAGGAUGAUUUUCUGUUAGACUGCCAUUUUGCACGGUCUCCCCCUUCCCAUCUGAUGUGUCCUGCCCCUCAGCUCUUUGCCUUAUCUGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000442218.2 | 3UTR | UGCACGGUCUCCCCCUUCCC |
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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62 hsa-miR-1245b-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT087132 | CRKL | CRK like proto-oncogene, adaptor protein | 2 | 2 | ||||||||
MIRT093398 | TMA16 | translation machinery associated 16 homolog | 2 | 2 | ||||||||
MIRT096092 | SFXN1 | sideroflexin 1 | 2 | 2 | ||||||||
MIRT097106 | TNPO1 | transportin 1 | 2 | 4 | ||||||||
MIRT241837 | SLC38A2 | solute carrier family 38 member 2 | 2 | 2 | ||||||||
MIRT271432 | ETNK1 | ethanolamine kinase 1 | 2 | 2 | ||||||||
MIRT329517 | E2F3 | E2F transcription factor 3 | 2 | 4 | ||||||||
MIRT444201 | SESN3 | sestrin 3 | 2 | 2 | ||||||||
MIRT445920 | SHOC2 | SHOC2, leucine rich repeat scaffold protein | 2 | 2 | ||||||||
MIRT450210 | PAIP1 | poly(A) binding protein interacting protein 1 | 2 | 2 | ||||||||
MIRT455192 | AGTRAP | angiotensin II receptor associated protein | 2 | 2 | ||||||||
MIRT455458 | EPB41L4B | erythrocyte membrane protein band 4.1 like 4B | 2 | 2 | ||||||||
MIRT459016 | UQCRH | ubiquinol-cytochrome c reductase hinge protein | 2 | 2 | ||||||||
MIRT461492 | KIAA1009 | centrosomal protein 162 | 1 | 1 | ||||||||
MIRT466306 | TIMM22 | translocase of inner mitochondrial membrane 22 | 2 | 2 | ||||||||
MIRT471143 | PHF19 | PHD finger protein 19 | 2 | 2 | ||||||||
MIRT473481 | MCFD2 | multiple coagulation factor deficiency 2 | 2 | 2 | ||||||||
MIRT473564 | MATR3 | matrin 3 | 2 | 2 | ||||||||
MIRT474013 | LRRC20 | leucine rich repeat containing 20 | 2 | 2 | ||||||||
MIRT475982 | GTPBP2 | GTP binding protein 2 | 2 | 2 | ||||||||
MIRT478926 | CPNE3 | copine 3 | 2 | 2 | ||||||||
MIRT479896 | CCDC117 | coiled-coil domain containing 117 | 2 | 2 | ||||||||
MIRT480115 | CALR | calreticulin | 2 | 2 | ||||||||
MIRT483127 | ONECUT3 | one cut homeobox 3 | 2 | 2 | ||||||||
MIRT484236 | IER2 | immediate early response 2 | 2 | 2 | ||||||||
MIRT492237 | SLC48A1 | solute carrier family 48 member 1 | 2 | 2 | ||||||||
MIRT496934 | CAMK4 | calcium/calmodulin dependent protein kinase IV | 2 | 2 | ||||||||
MIRT500438 | ZMAT3 | zinc finger matrin-type 3 | 2 | 2 | ||||||||
MIRT506263 | PDPK1 | 3-phosphoinositide dependent protein kinase 1 | 2 | 2 | ||||||||
MIRT525649 | NHSL2 | NHS like 2 | 2 | 2 | ||||||||
MIRT526691 | BAK1 | BCL2 antagonist/killer 1 | 2 | 2 | ||||||||
MIRT529667 | SLC28A1 | solute carrier family 28 member 1 | 2 | 2 | ||||||||
MIRT531152 | CYGB | cytoglobin | 2 | 2 | ||||||||
MIRT537002 | GTPBP10 | GTP binding protein 10 | 2 | 2 | ||||||||
MIRT537325 | FOXN3 | forkhead box N3 | 2 | 2 | ||||||||
MIRT537586 | ESYT2 | extended synaptotagmin 2 | 2 | 2 | ||||||||
MIRT538786 | C6orf89 | chromosome 6 open reading frame 89 | 2 | 2 | ||||||||
MIRT540286 | RGR | retinal G protein coupled receptor | 2 | 4 | ||||||||
MIRT552700 | YWHAH | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta | 2 | 2 | ||||||||
MIRT555670 | PGAM4 | phosphoglycerate mutase family member 4 | 2 | 2 | ||||||||
MIRT556823 | KDELR2 | KDEL endoplasmic reticulum protein retention receptor 2 | 2 | 2 | ||||||||
MIRT568686 | TOMM40 | translocase of outer mitochondrial membrane 40 | 2 | 2 | ||||||||
MIRT568851 | VPS53 | VPS53, GARP complex subunit | 2 | 2 | ||||||||
MIRT571973 | KIF21A | kinesin family member 21A | 2 | 2 | ||||||||
MIRT573973 | DDX21 | DExD-box helicase 21 | 2 | 2 | ||||||||
MIRT574260 | DOCK7 | dedicator of cytokinesis 7 | 2 | 2 | ||||||||
MIRT612180 | EMC3 | ER membrane protein complex subunit 3 | 2 | 2 | ||||||||
MIRT619387 | KLHL12 | kelch like family member 12 | 2 | 2 | ||||||||
MIRT625708 | SHROOM1 | shroom family member 1 | 2 | 2 | ||||||||
MIRT646803 | EVC2 | EvC ciliary complex subunit 2 | 2 | 2 | ||||||||
MIRT656992 | KCNN3 | potassium calcium-activated channel subfamily N member 3 | 2 | 2 | ||||||||
MIRT676250 | PARP2 | poly(ADP-ribose) polymerase 2 | 2 | 2 | ||||||||
MIRT682591 | CPA4 | carboxypeptidase A4 | 2 | 2 | ||||||||
MIRT687779 | KHSRP | KH-type splicing regulatory protein | 2 | 2 | ||||||||
MIRT690292 | ZNF154 | zinc finger protein 154 | 2 | 2 | ||||||||
MIRT692718 | MEAF6 | MYST/Esa1 associated factor 6 | 2 | 2 | ||||||||
MIRT700284 | RAN | RAN, member RAS oncogene family | 2 | 2 | ||||||||
MIRT708293 | ZNF24 | zinc finger protein 24 | 2 | 2 | ||||||||
MIRT709767 | GPR183 | G protein-coupled receptor 183 | 2 | 2 | ||||||||
MIRT720689 | LY6K | lymphocyte antigen 6 family member K | 2 | 2 | ||||||||
MIRT722784 | ACADSB | acyl-CoA dehydrogenase, short/branched chain | 2 | 2 | ||||||||
MIRT725414 | HNRNPU | heterogeneous nuclear ribonucleoprotein U | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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