pre-miRNA Information | |
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pre-miRNA | hsa-mir-16-2 |
Genomic Coordinates | chr3: 160404745 - 160404825 |
Description | Homo sapiens miR-16-2 stem-loop |
Comment | This entry represents a second putative hairpin precursor sequence for miR-16, located on chromosome 3 (see also MIR:MI0000070). The sequence was previously named mir-16-3 here and in references . |
RNA Secondary Structure | ![]() |
Associated Diseases | ![]() |
Mature miRNA Information | |||||||||||||||||||
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Mature miRNA | hsa-miR-16-2-3p | ||||||||||||||||||
Sequence | 53| CCAAUAUUACUGUGCUGCUUUA |74 | ||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||
Experiments | Cloned | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | CBS | ||||||||||||||||||||
Synonyms | HIP4 | ||||||||||||||||||||
Description | cystathionine-beta-synthase | ||||||||||||||||||||
Transcript | NM_000071 | ||||||||||||||||||||
Other Transcripts | NM_001178008 , NM_001178009 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on CBS | |||||||||||||||||||||
3'UTR of CBS (miRNA target sites are highlighted) |
>CBS|NM_000071|3'UTR 1 AGTCCGGAGCGCTGGGCGGTGCGGAGCGGGCCCGCCACCCTTGCCCACTTCTCCTTCGCTTTCCTGAGCCCTAAACACAC 81 GCGTGATTGGTAACTGCCTGGCCTGGCACCGTTATCCCTGCACACGGCACAGAGCATCCGTCTCCCCTCGTTAACACATG 161 GCTTCCTAAATGGCCCTGTTTACGGCCTATGAGATGAAATATGTGATTTTCTCTAATGTAACTTCCTCTTAGGATGTTTC 241 ACCAAGGAAATATTGAGAGAGAAGTCGGCCAGGTAGGATGAACACAGGCAATGACTGCGCAGAGTGGATTAAAGGCAAAA 321 GAGAGAAGAGTCCAGGAAGGGGCGGGGAGAAGCCTGGGTGGCTCAGCATCCTCCACGGGCTGCGCCGTCTGCTCGGGGCT 401 GAGCTGGCGGGAGCAGTTTGCGTGTTTGGGTTTTTTAATTGAGATGAAATTCAAATAACCTAAAAATCAATCACTTGAAA 481 GTGAACAATCAGCGGCATTTAGTACATCCAGAAAGTTGTGTAGGCACCACCTCTGTCACGTTCTGGAACATTCTGTCATC 561 ACCCCGTGAAGCAATCATTTCCCCTCCCGTCTTCCTCCTCCCCTGGCAACTGCTGATCGACTTTGTGTCTCTGTTGTCTA 641 AAATAGGTTTTCCCTGTTCTGGACATTTCATATAAATGGAATCACACAAAAAAAAAAAAAAAAAAAAA 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 | HEK293S |
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 GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb
... - 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 GSM1084065 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_AbnovaAb |
Location of target site | ENST00000398158.1 | 3UTR | AAAAAAGGGGAGAAAAU |
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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75 hsa-miR-16-2-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT004488 | RARB | retinoic acid receptor beta | ![]() |
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3 | 1 | |||||
MIRT038707 | NUCKS1 | nuclear casein kinase and cyclin dependent kinase substrate 1 | ![]() |
1 | 1 | |||||||
MIRT057208 | PPIF | peptidylprolyl isomerase F | ![]() |
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2 | 4 | ||||||
MIRT058726 | RSBN1 | round spermatid basic protein 1 | ![]() |
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2 | 8 | ||||||
MIRT074502 | NFATC2IP | nuclear factor of activated T-cells 2 interacting protein | ![]() |
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2 | 4 | ||||||
MIRT081544 | ZNF431 | zinc finger protein 431 | ![]() |
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2 | 4 | ||||||
MIRT096893 | ERBB2IP | erbb2 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT105124 | MYC | MYC proto-oncogene, bHLH transcription factor | ![]() |
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2 | 2 | ||||||
MIRT107898 | PTAR1 | protein prenyltransferase alpha subunit repeat containing 1 | ![]() |
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2 | 4 | ||||||
MIRT109432 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 6 | ||||||
MIRT166742 | PAPD7 | poly(A) RNA polymerase D7, non-canonical | ![]() |
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2 | 6 | ||||||
MIRT171257 | YWHAG | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma | ![]() |
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2 | 2 | ||||||
MIRT192760 | B2M | beta-2-microglobulin | ![]() |
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2 | 2 | ||||||
MIRT194905 | RBBP6 | RB binding protein 6, ubiquitin ligase | ![]() |
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2 | 8 | ||||||
MIRT215599 | SUB1 | SUB1 homolog, transcriptional regulator | ![]() |
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2 | 2 | ||||||
MIRT223632 | ATP6V1C1 | ATPase H+ transporting V1 subunit C1 | ![]() |
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2 | 4 | ||||||
MIRT241605 | AMOTL1 | angiomotin like 1 | ![]() |
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2 | 4 | ||||||
MIRT291174 | SH3GLB1 | SH3 domain containing GRB2 like, endophilin B1 | ![]() |
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2 | 2 | ||||||
MIRT444286 | ABCG2 | ATP binding cassette subfamily G member 2 (Junior blood group) | ![]() |
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2 | 2 | ||||||
MIRT463285 | ZFX | zinc finger protein, X-linked | ![]() |
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2 | 4 | ||||||
MIRT471759 | NUS1 | NUS1 dehydrodolichyl diphosphate synthase subunit | ![]() |
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2 | 8 | ||||||
MIRT479611 | CDC25A | cell division cycle 25A | ![]() |
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2 | 2 | ||||||
MIRT481497 | ARL6IP1 | ADP ribosylation factor like GTPase 6 interacting protein 1 | ![]() |
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2 | 8 | ||||||
MIRT483117 | SH3BP5 | SH3 domain binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT502279 | GRPEL2 | GrpE like 2, mitochondrial | ![]() |
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2 | 8 | ||||||
MIRT507838 | CCNT1 | cyclin T1 | ![]() |
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2 | 2 | ||||||
MIRT508179 | MTRNR2L6 | MT-RNR2-like 6 | ![]() |
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2 | 4 | ||||||
MIRT510576 | UBE2D3 | ubiquitin conjugating enzyme E2 D3 | ![]() |
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2 | 6 | ||||||
MIRT517853 | RPS4X | ribosomal protein S4, X-linked | ![]() |
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2 | 4 | ||||||
MIRT521690 | PRKAA1 | protein kinase AMP-activated catalytic subunit alpha 1 | ![]() |
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2 | 8 | ||||||
MIRT525070 | FRK | fyn related Src family tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT527082 | UBE2E3 | ubiquitin conjugating enzyme E2 E3 | ![]() |
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2 | 2 | ||||||
MIRT529552 | EI24 | EI24, autophagy associated transmembrane protein | ![]() |
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2 | 2 | ||||||
MIRT530426 | SULT1B1 | sulfotransferase family 1B member 1 | ![]() |
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2 | 2 | ||||||
MIRT533909 | TBC1D15 | TBC1 domain family member 15 | ![]() |
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2 | 2 | ||||||
MIRT536627 | IPO7 | importin 7 | ![]() |
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2 | 2 | ||||||
MIRT537647 | ERGIC2 | ERGIC and golgi 2 | ![]() |
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2 | 4 | ||||||
MIRT538512 | CLCN3 | chloride voltage-gated channel 3 | ![]() |
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2 | 2 | ||||||
MIRT539219 | ANP32E | acidic nuclear phosphoprotein 32 family member E | ![]() |
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2 | 6 | ||||||
MIRT539348 | AGO2 | argonaute 2, RISC catalytic component | ![]() |
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2 | 4 | ||||||
MIRT539954 | CCT4 | chaperonin containing TCP1 subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT541208 | HOXA10 | homeobox A10 | ![]() |
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2 | 2 | ||||||
MIRT543216 | TMEM117 | transmembrane protein 117 | ![]() |
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2 | 2 | ||||||
MIRT543399 | DROSHA | drosha ribonuclease III | ![]() |
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2 | 2 | ||||||
MIRT546648 | RPS6KA5 | ribosomal protein S6 kinase A5 | ![]() |
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2 | 2 | ||||||
MIRT546852 | RAB1A | RAB1A, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT549917 | MRPS30 | mitochondrial ribosomal protein S30 | ![]() |
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2 | 2 | ||||||
MIRT552998 | USP46 | ubiquitin specific peptidase 46 | ![]() |
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2 | 2 | ||||||
MIRT555254 | PREPL | prolyl endopeptidase-like | ![]() |
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2 | 2 | ||||||
MIRT555956 | NRIP1 | nuclear receptor interacting protein 1 | ![]() |
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2 | 2 | ||||||
MIRT557095 | HOXA9 | homeobox A9 | ![]() |
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2 | 2 | ||||||
MIRT561396 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT561654 | RNF219 | ring finger protein 219 | ![]() |
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2 | 2 | ||||||
MIRT563101 | PABPC4L | poly(A) binding protein cytoplasmic 4 like | ![]() |
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2 | 2 | ||||||
MIRT565979 | RNF44 | ring finger protein 44 | ![]() |
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2 | 2 | ||||||
MIRT572396 | CCDC14 | coiled-coil domain containing 14 | ![]() |
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2 | 2 | ||||||
MIRT574400 | TM9SF3 | transmembrane 9 superfamily member 3 | ![]() |
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2 | 2 | ||||||
MIRT607623 | VSNL1 | visinin like 1 | ![]() |
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2 | 2 | ||||||
MIRT610645 | CTGF | connective tissue growth factor | ![]() |
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2 | 2 | ||||||
MIRT623379 | LPP | LIM domain containing preferred translocation partner in lipoma | ![]() |
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2 | 2 | ||||||
MIRT624687 | AR | androgen receptor | ![]() |
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2 | 2 | ||||||
MIRT632089 | ALDH1A2 | aldehyde dehydrogenase 1 family member A2 | ![]() |
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2 | 2 | ||||||
MIRT644216 | CBS | cystathionine-beta-synthase | ![]() |
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2 | 2 | ||||||
MIRT647841 | BID | BH3 interacting domain death agonist | ![]() |
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2 | 2 | ||||||
MIRT651649 | WASF2 | WAS protein family member 2 | ![]() |
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2 | 2 | ||||||
MIRT689064 | AGMAT | agmatinase | ![]() |
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2 | 2 | ||||||
MIRT698150 | TNPO1 | transportin 1 | ![]() |
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2 | 2 | ||||||
MIRT700516 | PTPN14 | protein tyrosine phosphatase, non-receptor type 14 | ![]() |
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2 | 2 | ||||||
MIRT704081 | DYRK2 | dual specificity tyrosine phosphorylation regulated kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT705970 | ACBD5 | acyl-CoA binding domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT715694 | COMMD3-BMI1 | COMMD3-BMI1 readthrough | ![]() |
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2 | 2 | ||||||
MIRT717184 | BMI1 | BMI1 proto-oncogene, polycomb ring finger | ![]() |
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2 | 2 | ||||||
MIRT724607 | AP3B1 | adaptor related protein complex 3 beta 1 subunit | ![]() |
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2 | 2 | ||||||
MIRT724854 | IGFBP5 | insulin like growth factor binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT725401 | LRIG2 | leucine rich repeats and immunoglobulin like domains 2 | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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