pre-miRNA Information | |
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pre-miRNA | hsa-mir-3622b |
Genomic Coordinates | chr8: 27701673 - 27701767 |
Description | Homo sapiens miR-3622b stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3622b-3p | |||||||||||||||||||||||||||
Sequence | 58| UCACCUGAGCUCCCGUGCCUG |78 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas |
Gene Information | |||||||||||||||||||||
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Gene Symbol | Socs6 | ||||||||||||||||||||
Synonyms | 1500012M23Rik, 5830401B18Rik, AI447482, Cis4, Cish4, HSPC060, SOCS-4, SOCS-6, SSI4, STAI4, STATI4, Socs4 | ||||||||||||||||||||
Description | suppressor of cytokine signaling 6 | ||||||||||||||||||||
Transcript | NM_018821 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on Socs6 | |||||||||||||||||||||
3'UTR of Socs6 (miRNA target sites are highlighted) |
>Socs6|NM_018821|3'UTR 1 GAGATTTGGAGCCCTGTTTCTTGCACTTTGGGGTTCAGAAACAAGACTTGAGTACAGTTTACAGACTTACATCGCCATTG 81 AAGTCTTTGCTGCCATAACTTTTAGTTTTTATGTGTGAGAGTCATCAATTTGTTCAAGGGTGGGGAAGTGTCTGCAAGGC 161 GTCCTGAGTTTATTTTGGTTCTTGAAAAGGGATGCCTTTAGGGTTTAGAAGTGTGAGTTATCTTTCCTTAATGTGCAGAA 241 TAATCACAATGTGAATGACCAGATTCTCTTTAATGCCCCTTCCAGTCCTTTGCTGCTATCCACTGTGATTCTTATGCATT 321 AAAGCACATTTCATGTGTATTCAACCCTAAGTAAAGTTGAATGAAACTTAAATATAAATTGCTATGATGTTAAATGGCCC 401 AGTTGAATAAACGTGTGGGATAAAACATTTACATATACACTGAAAACTGATTTTTTTTAAGTCTCACACTTTAAAAGTGA 481 TTTGTTCAGAATTATGAATTAATACAATGTTGATAAATGGAATGCAAATCTGCAACATCTTTTAAAATACTTTTCTAAAT 561 TATTTTTTAAGGATGTGATAATTGTTTTGGTTGGGAGAAGTTGAATTGTTCTGTTGCCTTCATTTTCATCTTGTGGTTTG 641 TCTCTTTTGATAAATTGCCTTACATTAAAAATTGTAAACAAATATATACCCAATTTAGAAATTGTTGCCTTTTCTGTCAT 721 TAAACTCGGGTACAAATTGGCGTAACTTAAAAGCTCTGTAAAGCCCAAACAATTGTTACAAAAGTAAGATAACCCTGGTT 801 TTTGTGAGGTGTGTGTGTGTTCGTGTGTGTAAGAGAGAGAGAGATTTTTCAGTTACATATTTTATCTATGATTTCTTTAG 881 TAGATATTTTCTTCCATAAACTTGACAAAACAAGTTTCATAAATGAGTTGTATTTTCTTACATTAAAGTTTATATAAAGT 961 TGTAAACTGATCTGAATAGAAAGGTTATTTTAAAGTTGTCTTGACTTTCTTCTGTATAATCTTTACAGTGTGCTGTGTTT 1041 GACCATTCTAACTCTAAACCAACAACCTTGAATGACATCAGCTAAATAATTAAAAATTGTGATACATTATGTGAGAAAAA 1121 TTGTAAAACTATGTCTGATACCAGAAATAGTTTCCTGCTTGTGACTACCCTTTGAGGATAGCATTTTGGTTTATTTTAAA 1201 TTGGTTAATTTGTAAGTAGTCTGGCACCTCTACTTACTTATCATTGTGTTAGAGAATGATGAGACCAGGTTTTAAAAGTT 1281 ATTTTGGAATGTAGACTGTTGATTCAGT 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 GSM1013105. RNA binding protein: AGO. Condition:HS5-replicate-2
... - Balakrishnan I; Yang X; Brown J; et al., 2014, Stem cells (Dayton, Ohio). |
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miRNA-target interactions (Provided by authors) |
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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 GSM1013105 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HS5 / HS5-replicate-2 |
Location of target site | ENST00000395472.2 | 3UTR | UGGCCAGGCUGGUCUCGAACUCCUGACCUCAGGUGAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24038734 / GSE41272 |
CLIP-seq Viewer | Link |
102 hsa-miR-3622b-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT076713 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT080212 | PRKACB | protein kinase cAMP-activated catalytic subunit beta | ![]() |
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2 | 2 | ||||||
MIRT081398 | GTPBP3 | GTP binding protein 3, mitochondrial | ![]() |
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2 | 2 | ||||||
MIRT107158 | ZBTB43 | zinc finger and BTB domain containing 43 | ![]() |
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2 | 2 | ||||||
MIRT254071 | BACH1 | BTB domain and CNC homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT409790 | FOXO3 | forkhead box O3 | ![]() |
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2 | 2 | ||||||
MIRT448679 | MAPK9 | mitogen-activated protein kinase 9 | ![]() |
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2 | 2 | ||||||
MIRT450206 | ABHD15 | abhydrolase domain containing 15 | ![]() |
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2 | 2 | ||||||
MIRT486621 | PDK3 | pyruvate dehydrogenase kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT489267 | TTLL1 | tubulin tyrosine ligase like 1 | ![]() |
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2 | 2 | ||||||
MIRT493117 | MKNK2 | MAP kinase interacting serine/threonine kinase 2 | ![]() |
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2 | 4 | ||||||
MIRT494570 | BAK1 | BCL2 antagonist/killer 1 | ![]() |
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2 | 2 | ||||||
MIRT497395 | RALY | RALY heterogeneous nuclear ribonucleoprotein | ![]() |
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2 | 2 | ||||||
MIRT504900 | CCDC86 | coiled-coil domain containing 86 | ![]() |
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2 | 2 | ||||||
MIRT505192 | USP46 | ubiquitin specific peptidase 46 | ![]() |
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2 | 4 | ||||||
MIRT506522 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
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2 | 6 | ||||||
MIRT508162 | ABCC5 | ATP binding cassette subfamily C member 5 | ![]() |
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2 | 8 | ||||||
MIRT508545 | PARVG | parvin gamma | ![]() |
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2 | 4 | ||||||
MIRT509850 | BIRC5 | baculoviral IAP repeat containing 5 | ![]() |
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2 | 6 | ||||||
MIRT510088 | PPWD1 | peptidylprolyl isomerase domain and WD repeat containing 1 | ![]() |
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2 | 8 | ||||||
MIRT512094 | CRK | CRK proto-oncogene, adaptor protein | ![]() |
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2 | 4 | ||||||
MIRT515381 | RPL7 | ribosomal protein L7 | ![]() |
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2 | 2 | ||||||
MIRT519176 | SCO1 | SCO1, cytochrome c oxidase assembly protein | ![]() |
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2 | 2 | ||||||
MIRT519964 | ZCCHC8 | zinc finger CCHC-type containing 8 | ![]() |
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2 | 2 | ||||||
MIRT522292 | NKAP | NFKB activating protein | ![]() |
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2 | 2 | ||||||
MIRT523160 | HMGB2 | high mobility group box 2 | ![]() |
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2 | 4 | ||||||
MIRT525314 | FANCA | Fanconi anemia complementation group A | ![]() |
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2 | 2 | ||||||
MIRT528194 | PLEKHM2 | pleckstrin homology and RUN domain containing M2 | ![]() |
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2 | 2 | ||||||
MIRT532885 | ZNF451 | zinc finger protein 451 | ![]() |
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2 | 2 | ||||||
MIRT538209 | CYR61 | cysteine rich angiogenic inducer 61 | ![]() |
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2 | 2 | ||||||
MIRT539497 | ACTN4 | actinin alpha 4 | ![]() |
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2 | 2 | ||||||
MIRT554600 | RRAGC | Ras related GTP binding C | ![]() |
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2 | 2 | ||||||
MIRT562444 | DCTN6 | dynactin subunit 6 | ![]() |
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2 | 2 | ||||||
MIRT562748 | AOC3 | amine oxidase, copper containing 3 | ![]() |
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2 | 2 | ||||||
MIRT565798 | SEC14L5 | SEC14 like lipid binding 5 | ![]() |
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2 | 2 | ||||||
MIRT565838 | SCML2 | Scm polycomb group protein like 2 | ![]() |
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2 | 2 | ||||||
MIRT566072 | RCC2 | regulator of chromosome condensation 2 | ![]() |
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2 | 2 | ||||||
MIRT566104 | RBPJ | recombination signal binding protein for immunoglobulin kappa J region | ![]() |
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2 | 2 | ||||||
MIRT572407 | MRPS14 | mitochondrial ribosomal protein S14 | ![]() |
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2 | 2 | ||||||
MIRT576198 | Vsig2 | V-set and immunoglobulin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT576313 | Acbd7 | acyl-Coenzyme A binding domain containing 7 | ![]() |
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2 | 2 | ||||||
MIRT576651 | Mill2 | MHC I like leukocyte 2 | ![]() |
1 | 1 | |||||||
MIRT576859 | Socs6 | suppressor of cytokine signaling 6 | ![]() |
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2 | 2 | ||||||
MIRT606819 | BICD2 | BICD cargo adaptor 2 | ![]() |
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2 | 2 | ||||||
MIRT610738 | NUDT16 | nudix hydrolase 16 | ![]() |
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2 | 4 | ||||||
MIRT614798 | RORA | RAR related orphan receptor A | ![]() |
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2 | 2 | ||||||
MIRT619006 | NTMT1 | N-terminal Xaa-Pro-Lys N-methyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT619420 | NOS1AP | nitric oxide synthase 1 adaptor protein | ![]() |
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2 | 2 | ||||||
MIRT620405 | MYO1H | myosin IH | ![]() |
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2 | 2 | ||||||
MIRT624869 | ABHD13 | abhydrolase domain containing 13 | ![]() |
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2 | 2 | ||||||
MIRT633527 | ZFP30 | ZFP30 zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT633927 | DNAH9 | dynein axonemal heavy chain 9 | ![]() |
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2 | 2 | ||||||
MIRT636611 | CLIC5 | chloride intracellular channel 5 | ![]() |
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2 | 2 | ||||||
MIRT640616 | MIOX | myo-inositol oxygenase | ![]() |
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2 | 2 | ||||||
MIRT642605 | C14orf180 | chromosome 14 open reading frame 180 | ![]() |
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2 | 2 | ||||||
MIRT644624 | SRSF2 | serine and arginine rich splicing factor 2 | ![]() |
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2 | 2 | ||||||
MIRT655113 | PHLDA3 | pleckstrin homology like domain family A member 3 | ![]() |
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2 | 2 | ||||||
MIRT658976 | DNAJB5 | DnaJ heat shock protein family (Hsp40) member B5 | ![]() |
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2 | 4 | ||||||
MIRT661495 | CHMP1B | charged multivesicular body protein 1B | ![]() |
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2 | 2 | ||||||
MIRT662996 | TMEM59 | transmembrane protein 59 | ![]() |
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2 | 2 | ||||||
MIRT663075 | SFR1 | SWI5 dependent homologous recombination repair protein 1 | ![]() |
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2 | 2 | ||||||
MIRT665405 | WEE1 | WEE1 G2 checkpoint kinase | ![]() |
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2 | 2 | ||||||
MIRT666106 | SSR1 | signal sequence receptor subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT669562 | ALDOA | aldolase, fructose-bisphosphate A | ![]() |
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2 | 2 | ||||||
MIRT670070 | ZNF783 | zinc finger family member 783 | ![]() |
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2 | 2 | ||||||
MIRT671192 | ZNF891 | zinc finger protein 891 | ![]() |
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2 | 2 | ||||||
MIRT675361 | KLHL26 | kelch like family member 26 | ![]() |
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2 | 2 | ||||||
MIRT678857 | LINC00598 | long intergenic non-protein coding RNA 598 | ![]() |
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2 | 2 | ||||||
MIRT679443 | C19orf52 | translocase of inner mitochondrial membrane 29 | ![]() |
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2 | 2 | ||||||
MIRT684163 | ALDH1B1 | aldehyde dehydrogenase 1 family member B1 | ![]() |
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2 | 2 | ||||||
MIRT684543 | ZNF460 | zinc finger protein 460 | ![]() |
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2 | 2 | ||||||
MIRT684674 | SLC2A11 | solute carrier family 2 member 11 | ![]() |
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2 | 2 | ||||||
MIRT684971 | MINOS1 | mitochondrial inner membrane organizing system 1 | ![]() |
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2 | 2 | ||||||
MIRT686006 | NEK4 | NIMA related kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT687758 | KIAA1328 | KIAA1328 | ![]() |
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2 | 2 | ||||||
MIRT688961 | ATXN3 | ataxin 3 | ![]() |
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2 | 2 | ||||||
MIRT689409 | UQCR11 | ubiquinol-cytochrome c reductase, complex III subunit XI | ![]() |
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2 | 2 | ||||||
MIRT690001 | MMP17 | matrix metallopeptidase 17 | ![]() |
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2 | 2 | ||||||
MIRT690165 | ELP3 | elongator acetyltransferase complex subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT690202 | C5orf45 | MRN complex interacting protein | ![]() |
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2 | 2 | ||||||
MIRT690477 | ZNF33A | zinc finger protein 33A | ![]() |
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2 | 2 | ||||||
MIRT690566 | MICA | MHC class I polypeptide-related sequence A | ![]() |
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2 | 2 | ||||||
MIRT692160 | C10orf111 | chromosome 10 open reading frame 111 | ![]() |
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2 | 2 | ||||||
MIRT693430 | PLGLB2 | plasminogen-like B2 | ![]() |
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2 | 2 | ||||||
MIRT693547 | ZNF708 | zinc finger protein 708 | ![]() |
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2 | 2 | ||||||
MIRT693697 | PLGLB1 | plasminogen-like B1 | ![]() |
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2 | 2 | ||||||
MIRT695006 | HSPA6 | heat shock protein family A (Hsp70) member 6 | ![]() |
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2 | 2 | ||||||
MIRT698525 | TFRC | transferrin receptor | ![]() |
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2 | 2 | ||||||
MIRT699574 | SIKE1 | suppressor of IKBKE 1 | ![]() |
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2 | 2 | ||||||
MIRT703446 | FYTTD1 | forty-two-three domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT704397 | CTSS | cathepsin S | ![]() |
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2 | 2 | ||||||
MIRT704485 | CPT1A | carnitine palmitoyltransferase 1A | ![]() |
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2 | 2 | ||||||
MIRT709822 | STPG1 | sperm tail PG-rich repeat containing 1 | ![]() |
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2 | 2 | ||||||
MIRT710859 | COQ7 | coenzyme Q7, hydroxylase | ![]() |
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2 | 2 | ||||||
MIRT711893 | INSIG2 | insulin induced gene 2 | ![]() |
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2 | 2 | ||||||
MIRT713796 | CPLX2 | complexin 2 | ![]() |
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2 | 2 | ||||||
MIRT718800 | C1GALT1C1 | C1GALT1 specific chaperone 1 | ![]() |
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2 | 2 | ||||||
MIRT719501 | SEC24B | SEC24 homolog B, COPII coat complex component | ![]() |
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2 | 2 | ||||||
MIRT719722 | PDE6B | phosphodiesterase 6B | ![]() |
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2 | 2 | ||||||
MIRT722204 | URM1 | ubiquitin related modifier 1 | ![]() |
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2 | 2 | ||||||
MIRT723523 | CLPTM1L | CLPTM1 like | ![]() |
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2 | 2 | ||||||
MIRT725471 | GRAP2 | GRB2-related adaptor protein 2 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||
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