pre-miRNA Information | |
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pre-miRNA | hsa-mir-4436b-1 |
Genomic Coordinates | chr2: 110086433 - 110086523 |
Description | Homo sapiens miR-4436b-1 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | hsa-mir-4436b-2 |
Genomic Coordinates | chr2: 110284853 - 110284943 |
Description | Homo sapiens miR-4436b-2 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||
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Mature miRNA | hsa-miR-4436b-3p | ||||||
Sequence | 60| CAGGGCAGGAAGAAGUGGACAA |81 | ||||||
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 | Hmox1 | ||||||||||||||||||||
Synonyms | D8Wsu38e, HO-1, HO1, Hemox, Hmox, Hsp32 | ||||||||||||||||||||
Description | heme oxygenase 1 | ||||||||||||||||||||
Transcript | NM_010442 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on Hmox1 | |||||||||||||||||||||
3'UTR of Hmox1 (miRNA target sites are highlighted) |
>Hmox1|NM_010442|3'UTR 1 ATGCAATACTGGCCCCCAGGGGCTGTGAACTCTGTCCAATGTGGCCTTCTCTCTGTAAGGGAGAATCTTGCCTGGCTCTC 81 TTCTCTTGGGCCTCTAAGAAAGCTTTTGGGGTCCCTAGCCCACTCCCTGTGTTTCCTTTCTCTCTGGAATGGAGGGAGAT 161 ACCTGACACAGTTCCCTCACCAAAAGCACATCCAGCCAGTGGCCTGAACTTTGAAACCAGCAGCCCCAAATCCTGCAGCA 241 GAGCCCCAAAACTGGCCTGTAAAAGCAGCTGTTCTGAGCCCAGTGCCCATGGTTGTAAGCATCCATGTTGACTGACCACG 321 ACTGCTGTCCCCCAGTGCCATGGCCACTTTGATATCCGTTTCCAGACATTTCTGTCTCGTATTTCTGTCTTGTTTTTTAT 401 TATTTCCCCAGTTCTACCAGAGTAATGGTATTTTGTTGTTTTGTTTTGTCTTGTTTTTCCTAACAAAGTGGGGCTATCTT 481 TTGAGGGGTGGGTGGGAAAGAATTATTTAATAGTTGTAACCTTGGTCTCTAACTTCTGTGTGAAATAATAAATGGCATTA 561 TCTAACAGTCACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 | hMSC |
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 GSM1013110. RNA binding protein: AGO. Condition:hMSC-replicate-1
... - 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_002133 | 3UTR | AUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
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_002133 | 3UTR | AGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 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_002133 | 3UTR | AAGGAGCCUAUGGCAUCUUCCCCAACGAAAAGCACAUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 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_002133 | 3UTR | UAUGGCAUCUUCCCCAACGAAAAGCACAUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 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_002133 | 3UTR | CCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 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_002133 | 3UTR | AAGGAGCCUAUGGCAUCUUCCCCAACGAAAAGCACAUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 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_002133 | 3UTR | AAGGAGCCUAUGGCAUCUUCCCCAACGAAAAGCACAUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 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_002133 | 3UTR | CUAUGGCAUCUUCCCCAACGAAAAGCACAUCCAGGCAAUGGCCUAAACUUCAGAGGGGGCGAAGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 9 for dataset GSM1013110 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | hMSC / hMSC-replicate-1 |
Location of target site | ENST00000216117.8 | 3UTR | AGGGAUCAGCCCUGCCCUUCAGCAUCCUCAGUUCCUGCAGCAGAGCCUGGAAGACACCCUAAUGUGGCAGCUGUCUC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24038734 / GSE41272 |
CLIP-seq Viewer | Link |
87 hsa-miR-4436b-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT066957 | ATXN7L3B | ataxin 7 like 3B | ![]() |
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2 | 8 | ||||||
MIRT119284 | NABP1 | nucleic acid binding protein 1 | ![]() |
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2 | 6 | ||||||
MIRT128915 | KMT2A | lysine methyltransferase 2A | ![]() |
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2 | 2 | ||||||
MIRT150116 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT173040 | YTHDF3 | YTH N6-methyladenosine RNA binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT253117 | BCL2L12 | BCL2 like 12 | ![]() |
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2 | 2 | ||||||
MIRT256997 | RGMB | repulsive guidance molecule family member b | ![]() |
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2 | 2 | ||||||
MIRT259746 | SNX12 | sorting nexin 12 | ![]() |
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2 | 2 | ||||||
MIRT267278 | TMEM109 | transmembrane protein 109 | ![]() |
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2 | 2 | ||||||
MIRT441934 | C1orf109 | chromosome 1 open reading frame 109 | ![]() |
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2 | 2 | ||||||
MIRT443625 | CPSF2 | cleavage and polyadenylation specific factor 2 | ![]() |
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2 | 2 | ||||||
MIRT445757 | AGO1 | argonaute 1, RISC catalytic component | ![]() |
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2 | 2 | ||||||
MIRT447835 | CTIF | cap binding complex dependent translation initiation factor | ![]() |
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2 | 2 | ||||||
MIRT451230 | ZNF444 | zinc finger protein 444 | ![]() |
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2 | 2 | ||||||
MIRT451966 | TMPRSS5 | transmembrane protease, serine 5 | ![]() |
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2 | 2 | ||||||
MIRT453127 | HOXC4 | homeobox C4 | ![]() |
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2 | 2 | ||||||
MIRT454604 | RPL13A | ribosomal protein L13a | ![]() |
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2 | 2 | ||||||
MIRT455176 | SUV39H1 | suppressor of variegation 3-9 homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT455547 | GJB1 | gap junction protein beta 1 | ![]() |
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2 | 2 | ||||||
MIRT458197 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT458356 | NOC2L | NOC2 like nucleolar associated transcriptional repressor | ![]() |
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2 | 2 | ||||||
MIRT458923 | DNM2 | dynamin 2 | ![]() |
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2 | 2 | ||||||
MIRT461013 | SYT7 | synaptotagmin 7 | ![]() |
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2 | 2 | ||||||
MIRT461643 | ZSWIM4 | zinc finger SWIM-type containing 4 | ![]() |
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2 | 2 | ||||||
MIRT461997 | PACSIN1 | protein kinase C and casein kinase substrate in neurons 1 | ![]() |
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2 | 2 | ||||||
MIRT462367 | BCL7B | BCL tumor suppressor 7B | ![]() |
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2 | 2 | ||||||
MIRT464915 | TXNIP | thioredoxin interacting protein | ![]() |
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2 | 2 | ||||||
MIRT466311 | TIMM22 | translocase of inner mitochondrial membrane 22 | ![]() |
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2 | 2 | ||||||
MIRT466591 | TBC1D2B | TBC1 domain family member 2B | ![]() |
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2 | 2 | ||||||
MIRT467045 | SRSF1 | serine and arginine rich splicing factor 1 | ![]() |
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2 | 2 | ||||||
MIRT468750 | SDC2 | syndecan 2 | ![]() |
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2 | 2 | ||||||
MIRT468943 | RPS24 | ribosomal protein S24 | ![]() |
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2 | 2 | ||||||
MIRT469474 | REEP5 | receptor accessory protein 5 | ![]() |
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2 | 2 | ||||||
MIRT469913 | PTRF | caveolae associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT473325 | MEX3A | mex-3 RNA binding family member A | ![]() |
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2 | 2 | ||||||
MIRT473643 | MARK2 | microtubule affinity regulating kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT474064 | LMNB2 | lamin B2 | ![]() |
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2 | 2 | ||||||
MIRT474357 | KMT2D | lysine methyltransferase 2D | ![]() |
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2 | 2 | ||||||
MIRT475394 | ICMT | isoprenylcysteine carboxyl methyltransferase | ![]() |
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2 | 4 | ||||||
MIRT476335 | GLTSCR1L | BRD4 interacting chromatin remodeling complex associated protein like | ![]() |
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2 | 2 | ||||||
MIRT478651 | CTDNEP1 | CTD nuclear envelope phosphatase 1 | ![]() |
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2 | 2 | ||||||
MIRT479585 | CDC42SE1 | CDC42 small effector 1 | ![]() |
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2 | 2 | ||||||
MIRT479943 | CBX5 | chromobox 5 | ![]() |
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2 | 2 | ||||||
MIRT482001 | AMOTL2 | angiomotin like 2 | ![]() |
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2 | 2 | ||||||
MIRT482043 | AMER1 | APC membrane recruitment protein 1 | ![]() |
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2 | 2 | ||||||
MIRT483070 | EXT2 | exostosin glycosyltransferase 2 | ![]() |
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2 | 6 | ||||||
MIRT484323 | KCNH1 | potassium voltage-gated channel subfamily H member 1 | ![]() |
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2 | 4 | ||||||
MIRT487528 | GXYLT2 | glucoside xylosyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT489636 | ALS2CL | ALS2 C-terminal like | ![]() |
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2 | 2 | ||||||
MIRT490693 | SSTR1 | somatostatin receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT490871 | UPK2 | uroplakin 2 | ![]() |
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2 | 2 | ||||||
MIRT492582 | PPM1L | protein phosphatase, Mg2+/Mn2+ dependent 1L | ![]() |
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2 | 2 | ||||||
MIRT492945 | NEUROD2 | neuronal differentiation 2 | ![]() |
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2 | 2 | ||||||
MIRT498675 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 4 | ||||||
MIRT499349 | RAB25 | RAB25, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT502338 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 4 | ||||||
MIRT502976 | CCNL1 | cyclin L1 | ![]() |
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2 | 8 | ||||||
MIRT503706 | NUP62 | nucleoporin 62 | ![]() |
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2 | 2 | ||||||
MIRT505567 | SMUG1 | single-strand-selective monofunctional uracil-DNA glycosylase 1 | ![]() |
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2 | 2 | ||||||
MIRT507808 | CDKN1B | cyclin dependent kinase inhibitor 1B | ![]() |
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2 | 2 | ||||||
MIRT513242 | FBXO41 | F-box protein 41 | ![]() |
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2 | 6 | ||||||
MIRT513586 | EVX1 | even-skipped homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT525036 | FRK | fyn related Src family tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT531035 | TDGF1P3 | teratocarcinoma-derived growth factor 1 pseudogene 3 | ![]() |
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2 | 2 | ||||||
MIRT531939 | RBMS2 | RNA binding motif single stranded interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT534912 | PUM2 | pumilio RNA binding family member 2 | ![]() |
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2 | 2 | ||||||
MIRT535717 | N4BP1 | NEDD4 binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT540498 | ZMAT4 | zinc finger matrin-type 4 | ![]() |
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2 | 4 | ||||||
MIRT541465 | AURKA | aurora kinase A | ![]() |
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2 | 2 | ||||||
MIRT554328 | SH3GLB1 | SH3 domain containing GRB2 like, endophilin B1 | ![]() |
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2 | 2 | ||||||
MIRT561572 | SLC6A9 | solute carrier family 6 member 9 | ![]() |
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2 | 2 | ||||||
MIRT564715 | ZNF322P1 | zinc finger protein 322 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT576176 | Hmox1 | heme oxygenase 1 | ![]() |
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2 | 2 | ||||||
MIRT629712 | XKR4 | XK related 4 | ![]() |
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2 | 2 | ||||||
MIRT636182 | THBD | thrombomodulin | ![]() |
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2 | 2 | ||||||
MIRT646315 | MPHOSPH8 | M-phase phosphoprotein 8 | ![]() |
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2 | 2 | ||||||
MIRT649174 | IQSEC1 | IQ motif and Sec7 domain 1 | ![]() |
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2 | 2 | ||||||
MIRT666945 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | ![]() |
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2 | 2 | ||||||
MIRT684057 | FOLR1 | folate receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT687585 | MAU2 | MAU2 sister chromatid cohesion factor | ![]() |
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2 | 2 | ||||||
MIRT689953 | ZNF185 | zinc finger protein 185 with LIM domain | ![]() |
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2 | 2 | ||||||
MIRT704071 | SRCAP | Snf2 related CREBBP activator protein | ![]() |
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2 | 2 | ||||||
MIRT704327 | DCUN1D5 | defective in cullin neddylation 1 domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT705406 | ATP1B3 | ATPase Na+/K+ transporting subunit beta 3 | ![]() |
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2 | 2 | ||||||
MIRT710488 | CDH5 | cadherin 5 | ![]() |
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2 | 2 | ||||||
MIRT718241 | LCE1A | late cornified envelope 1A | ![]() |
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2 | 2 | ||||||
MIRT723182 | CDCA4 | cell division cycle associated 4 | ![]() |
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2 | 2 |