pre-miRNA Information | |
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pre-miRNA | hsa-mir-1284 |
Genomic Coordinates | chr3: 71541970 - 71542089 |
Synonyms | MIRN1284, hsa-mir-1284, MIR1284 |
Description | Homo sapiens miR-1284 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-1284 | ||||||||||||||||||||||||||||||||||||
Sequence | 30| UCUAUACAGACCCUGGCUUUUC |51 | ||||||||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||||||||
Experiments | Illumina | 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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Gene Information | |||||||||||||||||||||
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Gene Symbol | Pxdn | ||||||||||||||||||||
Synonyms | 2310075M15Rik, C85409, E330004E07, VPO1, mKIAA0230 | ||||||||||||||||||||
Description | peroxidasin | ||||||||||||||||||||
Transcript | NM_181395 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on Pxdn | |||||||||||||||||||||
3'UTR of Pxdn (miRNA target sites are highlighted) |
>Pxdn|NM_181395|3'UTR 1 TGTTCCCGAGCTTAGCTCCTCGAAGCTGGTCCACAGAATACTTGTGAGCCTAGATGACAACATGGGGAGCTTCAGACCAC 81 AGGACAAGTTGGGATCTCAGACATTTCAGGACCTCTGCTGTGCCATCGCAGAAGCAGCCGGGGCTGCTTCACACCCTGTG 161 TTTGTAGAAGGAAATTGAGCAGGCGGGAGTGGGTGCAGGCTCTGGCCCTCACTTCATGTTAGACTTCTCAGGTTTATATT 241 TAAGTGTTTTTAAATGGAAAATTGGTGCTACTATTAAATCACACAGTTGAGACATGGGTTTCGAAATTGCTTCGGCCTGA 321 TGATGCCACTTCTGTTTAAGCGAGGCAGAAGGTCTTTGACAGGCTTCATTTAAACAGAAGCATTTGGCAAATGGAACAGG 401 ATCTTATAAAATAATATCCTGGGCCAAAATCCCTACAGGGATACTAGGGCTTTCTCCCACTGCTCCCTCATGTCTGCCAT 481 CTTCCCCTTCAGGGCCCTTCAGCGTCTAATAACAATACCAACACAAACCTGCACCTTGCGACCATGTCCACCCTTCTACA 561 CAGGACTGTCACATTATCAAGCCACAGTTAGAAATAATCTTGTTTCCACTTAGAAAATGTGTAAATACTGCCTTGCTGTA 641 AATTGAATGTGAAATCCTTTGGTCCTATGCCATGTTGAGTGACCCGAATAGCCCCTTGCATCGGCAGGATGGTCTGCAGC 721 CACCACCTGCCTTGGTTCCTGGCCATGGTGTAGGGAGGGTGATGGTCTGCAGCCACCACCTGCCTTGGTTCCTGGCCATG 801 GTGTAGGGAGGGTGATTCACTCTCCAGGTCCTTTGAATAGGTGACAGACAGGCAGAGCCTGAATGTCAGGAAATTCCATT 881 GTATGAATGCTTTAAAGGAAAACGTTCCCTATACCTCATTATTTTTTATTGCATGATGTTTTATAAAAATTTGCCCATTT 961 TAGATGTTAGAAAAATTATTTCCACTATGCAAATTTCTTTTTAATTCAGTGAAAAGCAACTGTTATACCTCATAGTCTCT 1041 TGTTTTTAATTGACCAAAATATTCCATTCTATTCTCACAAGGTTCTGAGGTCTCTGCCTGAAAAAGCAAGTCTCACCCTA 1121 TAGACACTGATGTGCCCAGCACTACGTGCCAGCCATTGTGGGAACACAAGAGGGTCACCTGCCCAAGGGCTAGGGAGGAA 1201 GACCTCAAGAACACAGAGGAGGTGGAAAAGGACAAAATAGGTGCCATTTTAGGGAGACCATGGTCAGATAGGGGGATGCT 1281 CAGTTCCTTGCAGCCTCGGGCGGGCTTATGTTGGCACTAAGGCCATTGTGGAGTGTACTTATATGATCCCTATGCTGATA 1361 GGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTG 1441 TGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAA 1521 GCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGA 1601 AGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCT 1681 GGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCC 1761 AAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGC 1841 AGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCAT 1921 TGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTT 2001 CCTTGTATTCAGTCCATTACCAAAGAGGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCACATCGT 2081 TAAGTGGAAAAAAAAAAAAAAAAAAA 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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Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HS5 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
HITS-CLIP聽 data was present in GSM1013108. RNA binding protein: AGO. Condition:HS5-replicate-3
... - Balakrishnan I; Yang X; Brown J; et al., 2014, Stem cells (Dayton, Ohio). |
Article |
- Balakrishnan I; Yang X; Brown J; et al. - Stem cells (Dayton, Ohio), 2014
Regulation of hematopoietic stem cell proliferation, lineage commitment, and differentiation in adult vertebrates requires extrinsic signals provided by cells in the marrow microenvironment (ME) located within the bone marrow. Both secreted and cell-surface bound factors critical to this regulation have been identified, yet control of their expression by cells within the ME has not been addressed. Herein we hypothesize that microRNAs (miRNAs) contribute to their controlled expression. MiRNAs are small noncoding RNAs that bind to target mRNAs and downregulate gene expression by either initiating mRNA degradation or preventing peptide translation. Testing the role of miRNAs in downregulating gene expression has been difficult since conventional techniques used to define miRNA-mRNA interactions are indirect and have high false-positive and negative rates. In this report, a genome-wide biochemical technique (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation or HITS-CLIP) was used to generate unbiased genome-wide maps of miRNA-mRNA interactions in two critical cellular components of the marrow ME: marrow stromal cells and bone marrow endothelial cells. Analysis of these datasets identified miRNAs as direct regulators of JAG1, WNT5A, MMP2, and VEGFA; four factors that are important to ME function. Our results show the feasibility and utility of unbiased genome-wide biochemical techniques in dissecting the role of miRNAs in regulation of complex tissues such as the marrow ME.
LinkOut: [PMID: 24038734]
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CLIP-seq Support 1 for dataset GSM4903825 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / PID14_NS |
Location of target site | NM_012293 | 3UTR | CCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903826 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / PID21_NS |
Location of target site | NM_012293 | 3UTR | CAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903827 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / PID14_9124 |
Location of target site | NM_012293 | 3UTR | AGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903828 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / PID21_9124 |
Location of target site | NM_012293 | 3UTR | AGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 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_012293 | 3UTR | UGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 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_012293 | 3UTR | CUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 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_012293 | 3UTR | CCUGGGAACCUCUGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 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_012293 | 3UTR | CUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 9 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_012293 | 3UTR | UCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 10 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_012293 | 3UTR | UCUUCCCUGGGAACCUCUGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 11 for dataset GSM1013108 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HS5 / HS5-replicate-3 |
Location of target site | ENST00000252804.4 | 3UTR | UCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24038734 / GSE41272 |
CLIP-seq Viewer | Link |
46 hsa-miR-1284 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT035831 | PRRC2B | proline rich coiled-coil 2B | 1 | 1 | ||||||||
MIRT079621 | DNAJB4 | DnaJ heat shock protein family (Hsp40) member B4 | 2 | 2 | ||||||||
MIRT149901 | LDLR | low density lipoprotein receptor | 2 | 2 | ||||||||
MIRT182786 | TOR1AIP2 | torsin 1A interacting protein 2 | 2 | 2 | ||||||||
MIRT188827 | TMTC3 | transmembrane and tetratricopeptide repeat containing 3 | 2 | 2 | ||||||||
MIRT198187 | EIF4A1 | eukaryotic translation initiation factor 4A1 | 3 | 1 | ||||||||
MIRT245472 | ARID5B | AT-rich interaction domain 5B | 2 | 2 | ||||||||
MIRT252245 | PMAIP1 | phorbol-12-myristate-13-acetate-induced protein 1 | 2 | 6 | ||||||||
MIRT269363 | WEE1 | WEE1 G2 checkpoint kinase | 2 | 2 | ||||||||
MIRT320406 | HOXA9 | homeobox A9 | 2 | 4 | ||||||||
MIRT474722 | KIF13A | kinesin family member 13A | 2 | 6 | ||||||||
MIRT497926 | BTG1 | BTG anti-proliferation factor 1 | 2 | 2 | ||||||||
MIRT504264 | C1orf147 | chromosome 1 open reading frame 147 | 2 | 4 | ||||||||
MIRT520449 | TSPAN2 | tetraspanin 2 | 2 | 4 | ||||||||
MIRT524092 | DNAJB14 | DnaJ heat shock protein family (Hsp40) member B14 | 2 | 4 | ||||||||
MIRT528639 | SENP6 | SUMO1/sentrin specific peptidase 6 | 2 | 2 | ||||||||
MIRT537385 | FGF2 | fibroblast growth factor 2 | 2 | 2 | ||||||||
MIRT538902 | BRI3BP | BRI3 binding protein | 2 | 2 | ||||||||
MIRT542095 | KCNK10 | potassium two pore domain channel subfamily K member 10 | 2 | 6 | ||||||||
MIRT543976 | PRR23A | proline rich 23A | 2 | 2 | ||||||||
MIRT549625 | ADCYAP1 | adenylate cyclase activating polypeptide 1 | 2 | 4 | ||||||||
MIRT554298 | SIPA1L2 | signal induced proliferation associated 1 like 2 | 2 | 2 | ||||||||
MIRT554872 | RCAN2 | regulator of calcineurin 2 | 2 | 2 | ||||||||
MIRT567623 | FAM210A | family with sequence similarity 210 member A | 2 | 2 | ||||||||
MIRT571137 | TTC33 | tetratricopeptide repeat domain 33 | 2 | 2 | ||||||||
MIRT576361 | Pxdn | peroxidasin | 2 | 2 | ||||||||
MIRT611088 | PHF8 | PHD finger protein 8 | 2 | 2 | ||||||||
MIRT612380 | TCTE1 | t-complex-associated-testis-expressed 1 | 2 | 4 | ||||||||
MIRT613725 | MTPN | myotrophin | 2 | 2 | ||||||||
MIRT614627 | YAE1D1 | Yae1 domain containing 1 | 2 | 2 | ||||||||
MIRT615818 | KIAA1549L | KIAA1549 like | 2 | 2 | ||||||||
MIRT620949 | TBCK | TBC1 domain containing kinase | 2 | 2 | ||||||||
MIRT622339 | SCN4A | sodium voltage-gated channel alpha subunit 4 | 2 | 2 | ||||||||
MIRT623219 | MTA3 | metastasis associated 1 family member 3 | 2 | 4 | ||||||||
MIRT628932 | SLC1A4 | solute carrier family 1 member 4 | 2 | 2 | ||||||||
MIRT632121 | FKBP9 | FK506 binding protein 9 | 2 | 2 | ||||||||
MIRT635877 | COX17 | COX17, cytochrome c oxidase copper chaperone | 2 | 2 | ||||||||
MIRT636485 | IKBKG | inhibitor of nuclear factor kappa B kinase subunit gamma | 2 | 2 | ||||||||
MIRT653097 | SRSF7 | serine and arginine rich splicing factor 7 | 2 | 2 | ||||||||
MIRT655048 | PKN2 | protein kinase N2 | 2 | 2 | ||||||||
MIRT686946 | SFT2D3 | SFT2 domain containing 3 | 2 | 2 | ||||||||
MIRT692724 | INPP5B | inositol polyphosphate-5-phosphatase B | 2 | 2 | ||||||||
MIRT697282 | ZNF800 | zinc finger protein 800 | 2 | 2 | ||||||||
MIRT698995 | SPAG9 | sperm associated antigen 9 | 2 | 2 | ||||||||
MIRT704462 | CRNKL1 | crooked neck pre-mRNA splicing factor 1 | 2 | 2 | ||||||||
MIRT715163 | FIG4 | FIG4 phosphoinositide 5-phosphatase | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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