pre-miRNA Information | |
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pre-miRNA | hsa-mir-4524a |
Genomic Coordinates | chr17: 69099564 - 69099632 |
Description | Homo sapiens miR-4524a stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4524a-5p | ||||||||||||
Sequence | 6| AUAGCAGCAUGAACCUGUCUCA |27 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | Illumina | ||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | BTN3A3 | ||||||||||||||||||||
Synonyms | BTF3, BTN3.3 | ||||||||||||||||||||
Description | butyrophilin subfamily 3 member A3 | ||||||||||||||||||||
Transcript | NM_006994 | ||||||||||||||||||||
Other Transcripts | NM_197974 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on BTN3A3 | |||||||||||||||||||||
3'UTR of BTN3A3 (miRNA target sites are highlighted) |
>BTN3A3|NM_006994|3'UTR 1 TATTCATTCCATTATTCCATATGACAGTTGTTTTGAGTTTCGTACCACCTTATTGTCCCCTTATACAGATAAGGAAACTG 81 GGGTGCAGAAAGGTGAATTAACTTTACAAAGTAGACATGACAAGTGAACAGCAGAGCTGGGATCTAAACAGCAATAACTA 161 ACATTAACAGAGAATTTAAAATGTTCTTAGTGCTGTGTTATAAGCTTTGGTGGATGTCACTCCTTTAATCCTCACAACAC 241 CCTGTCGGGTAGTCATATTTTGCAAGTATGGAAGCTGAGGCAGGGCAACATGAAGTAACTTACATAACTCATACAGTAAT 321 TTGTGCAGTTGGGAGATGTTCAGCCTTAGTCCCTGGCTAATTGCCTGTTCTTTTCCAGCCTGATTTTTTTTCCCACAGGA 401 AGAGCCCACATGTAGCCCTGAGGTTTCCTTCCCAGGACAGCTGCAGGGTAGAGATCATTTTAAGTGCTTGTGGAGTTGAC 481 ATCCCTATTGACTCTTTCCCAGCTGATATCAGAGACTTAGACCCAGCACTCCTTGGATTAGCTCTGCAGAGTGTCTTGGT 561 TGAGAGAATAACCTCATAGTACCAACATGACATGTGACTTGGAAAGAGACTAGAGGCCACACTTGATAAATCATGGGGCA 641 CAGATATGTTCCCACCCAACAAATGTGATAAGTGATTGTGCAGCCAGAGCCAGCCTTCCTTCAATCAAGGTTTCCAGGCA 721 GAGCAAATACCCTAGAGATTCTCTGTGATATAGGAAATTTGGATCAAGGAAGCTAAAAGAATTACAGGGATGTTTTTAAT 801 CCCACTATGGACTCAGTCTCCTGGAAATAGGTCTGTCCACTCCTGGTCATTGGTGGATGTTAAACCCATATTCCTTTCAA 881 CTGCTGCCTGCTAGGGAAAACTGCTCCTCATTATCATCACTATTATTGCTCACCACTGTATCCCCTCTACTTGGCAAGTG 961 GTTGTCAAGTTCTAGTTGTTCAATAAATGTGTTAATAATGCTTAAAAAAAAAAAAAAAAAA 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 | HEK293 | ||||||
Disease | 10384.0 | ||||||
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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CLIP-seq Support 1 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000380591.3 | 3UTR | UUACUGGGAGCUGCUAUUUUAUAUUAUGACUGCUUUUUAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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180 hsa-miR-4524a-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT055251 | CNNM2 | cyclin and CBS domain divalent metal cation transport mediator 2 | ![]() |
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2 | 2 | ||||||
MIRT055826 | PLEKHA1 | pleckstrin homology domain containing A1 | ![]() |
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2 | 2 | ||||||
MIRT060573 | CCND1 | cyclin D1 | ![]() |
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2 | 2 | ||||||
MIRT061013 | C1ORF21 | chromosome 1 open reading frame 21 | ![]() |
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2 | 6 | ||||||
MIRT064694 | CCND2 | cyclin D2 | ![]() |
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2 | 4 | ||||||
MIRT075268 | SNTB2 | syntrophin beta 2 | ![]() |
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2 | 4 | ||||||
MIRT079668 | NAPG | NSF attachment protein gamma | ![]() |
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2 | 12 | ||||||
MIRT081651 | CCNE1 | cyclin E1 | ![]() |
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2 | 4 | ||||||
MIRT082996 | PNPLA6 | patatin like phospholipase domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT083463 | RALGAPB | Ral GTPase activating protein non-catalytic beta subunit | ![]() |
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2 | 4 | ||||||
MIRT085755 | RIF1 | replication timing regulatory factor 1 | ![]() |
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2 | 2 | ||||||
MIRT086022 | UBR3 | ubiquitin protein ligase E3 component n-recognin 3 (putative) | ![]() |
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2 | 2 | ||||||
MIRT087431 | ZNRF3 | zinc and ring finger 3 | ![]() |
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2 | 2 | ||||||
MIRT088786 | SOCS5 | suppressor of cytokine signaling 5 | ![]() |
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2 | 2 | ||||||
MIRT089221 | ACTR2 | ARP2 actin related protein 2 homolog | ![]() |
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2 | 2 | ||||||
MIRT093696 | PI4K2B | phosphatidylinositol 4-kinase type 2 beta | ![]() |
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2 | 6 | ||||||
MIRT095090 | SEC24A | SEC24 homolog A, COPII coat complex component | ![]() |
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2 | 4 | ||||||
MIRT096249 | CANX | calnexin | ![]() |
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2 | 2 | ||||||
MIRT100215 | PPP1R11 | protein phosphatase 1 regulatory inhibitor subunit 11 | ![]() |
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2 | 2 | ||||||
MIRT100746 | VEGFA | vascular endothelial growth factor A | ![]() |
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2 | 12 | ||||||
MIRT100904 | CD2AP | CD2 associated protein | ![]() |
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2 | 2 | ||||||
MIRT102647 | UBN2 | ubinuclein 2 | ![]() |
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2 | 10 | ||||||
MIRT103882 | FOXK1 | forkhead box K1 | ![]() |
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2 | 2 | ||||||
MIRT104246 | DMTF1 | cyclin D binding myb like transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT106310 | ZFHX4 | zinc finger homeobox 4 | ![]() |
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2 | 6 | ||||||
MIRT107696 | RECK | reversion inducing cysteine rich protein with kazal motifs | ![]() |
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2 | 2 | ||||||
MIRT114943 | CHAC1 | ChaC glutathione specific gamma-glutamylcyclotransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT117671 | SCAMP4 | secretory carrier membrane protein 4 | ![]() |
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2 | 2 | ||||||
MIRT133799 | SKI | SKI proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT140167 | SPRED1 | sprouty related EVH1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT142279 | DCTN5 | dynactin subunit 5 | ![]() |
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2 | 8 | ||||||
MIRT143288 | N4BP1 | NEDD4 binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT165939 | CREBRF | CREB3 regulatory factor | ![]() |
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2 | 2 | ||||||
MIRT175251 | PSAT1 | phosphoserine aminotransferase 1 | ![]() |
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2 | 6 | ||||||
MIRT186381 | PNRC2 | proline rich nuclear receptor coactivator 2 | ![]() |
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2 | 2 | ||||||
MIRT191470 | PPM1A | protein phosphatase, Mg2+/Mn2+ dependent 1A | ![]() |
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2 | 2 | ||||||
MIRT196480 | TAOK1 | TAO kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT201470 | SNRPB2 | small nuclear ribonucleoprotein polypeptide B2 | ![]() |
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2 | 8 | ||||||
MIRT204615 | HSPE1-MOB4 | HSPE1-MOB4 readthrough | ![]() |
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2 | 8 | ||||||
MIRT204646 | MOB4 | MOB family member 4, phocein | ![]() |
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2 | 8 | ||||||
MIRT204749 | BZW1 | basic leucine zipper and W2 domains 1 | ![]() |
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2 | 12 |