pre-miRNA Information | |
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pre-miRNA | hsa-mir-3937 |
Genomic Coordinates | chrX: 39661216 - 39661321 |
Description | Homo sapiens miR-3937 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||
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Mature miRNA | hsa-miR-3937 | |||||||||||||||||||||
Sequence | 61| ACAGGCGGCUGUAGCAAUGGGGG |83 | |||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | SRCIN1 | ||||||||||||||||||||
Synonyms | P140, SNIP | ||||||||||||||||||||
Description | SRC kinase signaling inhibitor 1 | ||||||||||||||||||||
Transcript | NM_025248 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SRCIN1 | |||||||||||||||||||||
3'UTR of SRCIN1 (miRNA target sites are highlighted) |
>SRCIN1|NM_025248|3'UTR 1 AAGCCCCTCACCCCGCTGCCCCGCCTGTCCCCCTCCCTCACTCCTGCCATTTCTCCCCTCTCTTCCTTCATCTCCACCCC 81 ACCCCACCCTACTCTCCAGACGCCCTGAGGGGTGTGCCCTGAAGAGGAGGGTGCGGCCCTCCTCAGCGACCCCTACCCAT 161 CATCTGTTGGTGTTTTTGGTTTTGTTTTTTTTTTTTTTTTTAACAATTAACTTTTAATTATCTTTTTTTAAACAGTAAAA 241 CTAAAAACCAAACACACCACCTTCCTTGATCCCAGCTGGCCTCTCGCTGGCCGCACCTGTCACATCTCTCCTTCTTCTCT 321 TTCACCACTCTTTCCCCCAGTCCATCCTGAAGCTCCTGCACCCCCTTCCCGCCTTCCCCTCACTTCCCAAGAATACTCCA 401 AACAAACTCTGAACCACGGAGACTTGGAGCAGTGGGAGACCCCTCTCCCGTTTCTCGATACCTTCCTGGAGGAACGCGGG 481 GACATCGGACCAACCCATACATCAAGCCAGAGAGCGGGGCTTAGGGAGACTGGCCTTGGAGATGCCCCACTCCCTGTCTA 561 AGCTCCGACAAGACTGTGACTTCCTCTGTGGCTGCTCTGCCTCCTCCCACTCACACCCAAGTGGGCCTGGAGTAGAGACG 641 GACAGGCTGGAGACGAGGCCGGAGTTTGAGAGGCCTCAGGGTGGGTGTGAGGCCATGGAGTCTGTATCCCTGGGGAGGCG 721 CTGGCCTCCTGGGCCTTGCCGTCCAGTGGGGAGTGGAGGGCAGAGGCCCTTTGGTCTGCTGGCTGTGGAGGGTGGGTTGC 801 ACGGACAGCCGGATATCGGGGACACTGCCTTGGGAGAGGGCGGCCCGGACGGGTATTTGGTACTTTTAGTTTCCTGATTT 881 AGCACTTTAAATGGCATTAACTTATTGAATGGGGATGGGGTGGGCAAGAGTGAGGGGCCTAGAAAACCAGGTTTTGTGGC 961 TTGCAGTTGGGGGAAGGGTCTGGTTTGAGGGAAATGGGAGGGTCGAGAGGGGCTTGACGGGGAGCACTGAAGACACCTGG 1041 GACCCGCAGGTGGGGTGACTTGAACTTCAGTCATCCTCTTGGCAATTTGAGGGTTTTCCCAGGAAAGGATGAGACGTAGT 1121 TTTTCAATGGGGCTCTGGTGACCCTGGTGAGATGTCTGAAGGTCCCTGAGGCCTGACCATCCAGCCAGCGCCCCTGGCCT 1201 GTGGACGCCCTGCCTGCCCTGCAGAGGCGGTTGGCAGTGCCGCCTGGCTTTTGGCCGGGTCCTGGGGAGGCAGAGAGAGG 1281 CCAATTTTGGTTCTCACTCCTGGCCCCCCAGAGGGCACAGTGAGGAGCCGGTAGGGAGAGGATAGGAGAAGAGGAGGAGG 1361 AGGAGCGGGGTCCCCGGCCGCAGGATTCCCACTTGGAGCACAAAGTGAAGTAAGCACAGGGGAGGGGGACTAGAATCAGT 1441 CCCCCATAGCAAGCACAGAAAGGAGGAGCTGCGCAGAAGGCAGAGCCCCCCAGACCCTGGGGCCTGGCTGGGGAAGGTCC 1521 GCACCTGGGGAGAGCTGGGAGCTGTTGAAGGTTTGGGGGGAGGGGAAACGGGTTGTGTTTCTTCATTTCTTTTTTTGTTT 1601 TTGCCTTTGTTGGTTCATCCTTGTTTTCTAGCTTTGGATCATTTTTGTACCAAGGCGAGCAAGCCTTTTTGAAAAATAAC 1681 AAAAGAGGAAAAAAAAAATCCCTCCTGGAAAAAAAAAAAAACCCTGGAAAATAGAAAAAAAAAAAAGGACCTCATAAATG 1761 ATGCAATTACTTTTAATTGCAGGCAACTCTTTACATTTAAGTGAAGTGTCTTAACATTTTATATTGTTTTAAAAATATAT 1841 TTACATATTATATATATAATATACGTAATATAAATATATATAAATATTTAAAAAAGAAAAAAAAAAGAAAACCACGGCAC 1921 TCTCCCTGGCCACTGTTTTGGCGGGGGAGGGGGGCTGGGGGGCGGGCACGTCGGCCTGGCTTCTGTGGTCCCAGTGAAAT 2001 GGTCTGGTTTGATTTGGCTGTACAGAGACCCCCTGACTTGGGAGGGGAGGGGGGAGTGGTGCCCCCTCCTCCCTCCACTC 2081 CATTACTCTCTGCTTGCTACTTCGCTTGCCCCCAGCTCCCACCCTCAGCCCTGTGACTGGAATGTGTGCCCCACCGTCAT 2161 TGTCCTGAGTTGAATGTCCCTTTGTGGGGGAGGTGGGGGGGGCAGTGTCCATCCACGAAGGGGCAGAAGGAGGGAGCCAC 2241 GTGCCCCGCCCCACCCGCTCGGGTGAAGCCCAGTGGGATTTGCATCTTTCTTTCTCTTTGGTTCCTGCACATTTATGGGC 2321 TGGGAGGCATCCGTGTGGAATTGCGTGCAGCCTGTGTGTGTGCTGGCACAAGCCCATGCACTGTGTGTGCAGACGCATGG 2401 GGCCTGCACCCACAGGCATGGCCGAGCACATGTGTGGGGGAAGGCGTGGGCACATAGGTGCATGTAACCTGTTTGGGCAT 2481 TGGCACGTGCCTACCTGCATGTTAGCGTGAGAGGAGCTTTGTGTGTGAGAACATGTGTAATGTGTGTGCAGACATGCCGA 2561 GAGCCAGAGACTTGTGTGTGGGCCACGTACATGTGGATAGAGACGCATACATGGAGGTGCATGTAATCTGTGTCTCCGAG 2641 TGTGTGTGTGCAGGTATGTGTGCTGGTGCAGACCCAAGTGTGTGGGTGTGCCTCTGTGTGCGTGTGTTCCATCATCCCTG 2721 CACCACTGGCTCCAGATCCCTTCCTGAGCCCCCGTCCCCGCTGGCCCTCTCACAGCCTGCAGCACATCAGTGCCCCCAGC 2801 TGCATGCGCCTCGCTGCTCTGTCCATCAGTGTGTGCTTGACCAAGAGAAAACTAAGACGTCTCGGGGGACCCCTGTACCT 2881 GGTCCTCTCAGCCCCCGCCCACTGTGCTGTGTTACTCGCATGGGGGATTTCCTGCCCCTTCCACAATATGCTGTTTCCCC 2961 AGGAGCCTCAGGCCTGAGGCTCTGAGTGGGGTCCCCAGGGGGCCCCCCGGGGTGAGCCCCGGCTCCACACCCTGCCCCAT 3041 CCACCCTGTAGGGCCCATGTTGGTGTAGCAGTGATGGCTTCTGTGGATATTCTGTGACCTCTGTCGGTGTAACTTGACAA 3121 TTTCTAAATGGAAAAGGGTTGCTGTGTTTTCTCTGTCTCTCTTTTTTAATGTCCTTTTTTCTTCTCCCCCGCTCCCTGCT 3201 CTCTTTCCTTTTCAGTTTTTCTAGCCAAGTGTTTGGGGCTTTAATAAAACTTGTTTCTTTTTCCTCTCCTGGA 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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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 GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000264659.7 | 3UTR | CCGCCUGUCCCCCUCCC |
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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40 hsa-miR-3937 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT332487 | CD81 | CD81 molecule | 2 | 2 | ||||||||
MIRT441327 | NDUFA11 | NADH:ubiquinone oxidoreductase subunit A11 | 2 | 4 | ||||||||
MIRT454032 | EIF3CL | eukaryotic translation initiation factor 3 subunit C like | 2 | 2 | ||||||||
MIRT458086 | EIF3C | eukaryotic translation initiation factor 3 subunit C | 2 | 2 | ||||||||
MIRT460785 | VPS37B | VPS37B, ESCRT-I subunit | 2 | 2 | ||||||||
MIRT463150 | ZNF385A | zinc finger protein 385A | 2 | 4 | ||||||||
MIRT467162 | SREBF2 | sterol regulatory element binding transcription factor 2 | 2 | 2 | ||||||||
MIRT469618 | RAI1 | retinoic acid induced 1 | 2 | 4 | ||||||||
MIRT472258 | NFIC | nuclear factor I C | 2 | 2 | ||||||||
MIRT487587 | FAM83H | family with sequence similarity 83 member H | 2 | 4 | ||||||||
MIRT489302 | B4GALNT4 | beta-1,4-N-acetyl-galactosaminyltransferase 4 | 2 | 4 | ||||||||
MIRT489741 | GNAI2 | G protein subunit alpha i2 | 2 | 4 | ||||||||
MIRT490038 | PCSK4 | proprotein convertase subtilisin/kexin type 4 | 2 | 2 | ||||||||
MIRT490767 | SRCIN1 | SRC kinase signaling inhibitor 1 | 2 | 2 | ||||||||
MIRT491750 | SEMA3F | semaphorin 3F | 2 | 2 | ||||||||
MIRT492690 | PHYHIP | phytanoyl-CoA 2-hydroxylase interacting protein | 2 | 2 | ||||||||
MIRT504843 | RRP36 | ribosomal RNA processing 36 | 2 | 4 | ||||||||
MIRT510116 | IRAK3 | interleukin 1 receptor associated kinase 3 | 2 | 8 | ||||||||
MIRT525313 | FANCA | Fanconi anemia complementation group A | 2 | 4 | ||||||||
MIRT569801 | IGDCC3 | immunoglobulin superfamily DCC subclass member 3 | 2 | 2 | ||||||||
MIRT570224 | SLC27A1 | solute carrier family 27 member 1 | 2 | 2 | ||||||||
MIRT629378 | FAHD1 | fumarylacetoacetate hydrolase domain containing 1 | 2 | 2 | ||||||||
MIRT633104 | CBX5 | chromobox 5 | 2 | 2 | ||||||||
MIRT645036 | ATAD3C | ATPase family, AAA domain containing 3C | 2 | 2 | ||||||||
MIRT660973 | ABI2 | abl interactor 2 | 2 | 2 | ||||||||
MIRT671225 | CLSTN1 | calsyntenin 1 | 2 | 2 | ||||||||
MIRT672046 | SMTNL2 | smoothelin like 2 | 2 | 2 | ||||||||
MIRT677314 | CPSF2 | cleavage and polyadenylation specific factor 2 | 2 | 2 | ||||||||
MIRT678290 | PTRH2 | peptidyl-tRNA hydrolase 2 | 2 | 2 | ||||||||
MIRT693477 | ZNF707 | zinc finger protein 707 | 2 | 2 | ||||||||
MIRT693576 | PIGR | polymeric immunoglobulin receptor | 2 | 2 | ||||||||
MIRT696832 | PLLP | plasmolipin | 2 | 2 | ||||||||
MIRT700149 | RNF115 | ring finger protein 115 | 2 | 2 | ||||||||
MIRT703760 | FAM118A | family with sequence similarity 118 member A | 2 | 2 | ||||||||
MIRT705798 | ALDH6A1 | aldehyde dehydrogenase 6 family member A1 | 2 | 2 | ||||||||
MIRT709105 | SEPT4 | septin 4 | 2 | 2 | ||||||||
MIRT710235 | ARMCX6 | armadillo repeat containing, X-linked 6 | 2 | 2 | ||||||||
MIRT711422 | EPHA4 | EPH receptor A4 | 2 | 2 | ||||||||
MIRT712529 | CYTH2 | cytohesin 2 | 2 | 2 | ||||||||
MIRT714081 | ZNF532 | zinc finger protein 532 | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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