pre-miRNA Information | |
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pre-miRNA | hsa-mir-4699 |
Genomic Coordinates | chr12: 81158388 - 81158461 |
Description | Homo sapiens miR-4699 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||
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Mature miRNA | hsa-miR-4699-3p | |||||||||||||||
Sequence | 46| AAUUUACUCUGCAAUCUUCUCC |67 | |||||||||||||||
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 | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | AKAP1 | ||||||||||||||||||||
Synonyms | AKAP, AKAP121, AKAP149, AKAP84, D-AKAP1, PPP1R43, PRKA1, SAKAP84, TDRD17 | ||||||||||||||||||||
Description | A-kinase anchoring protein 1 | ||||||||||||||||||||
Transcript | NM_003488 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on AKAP1 | |||||||||||||||||||||
3'UTR of AKAP1 (miRNA target sites are highlighted) |
>AKAP1|NM_003488|3'UTR 1 CCCCCATGCTGCTTCCTGAGAGTCTTTTTTTGCACTGTTGAAATTGGGCTTGGCACTCAAGTCAAAGATGAACATCGGAA 81 TAACAAACATTGTCCTCTCCAGAAAGTCCTTTCTTTCTCCATACTGTAGTCCTATTGAGAAGACATTTCGTCTCTGAGAA 161 AAAAGGATGGAACTATGGGTTCTCTTCGCAAAGCCAAAGGATAGTGTTTAACAAGCCAGCTGGCTTATGCTGGTTCTCAG 241 CTGTTTAAAAAAAAAAAAAAAAAGGAATAGAAACAGTTTCAACCAGATTGTCCTATTCCCCCTGTTCCATTCCCCTCTTC 321 TTCCTTCTATCTCCTTCCCCGGCAAAAACCAAACAAACTGGCAGACAGGCCAGGGATGTATGTTGCTTGCTTGAGAGGGT 401 TTCTTTTACTTCAAAATCTTTCTTCAGGGAGCAAGACATGAACTGACTAATTGGTATCCACTACTTGTACAGCTTACATA 481 AATGAGTTGATGATATTTAACCAGTTTTTATAAACTTCATTTAGGTCTCTAAACACAGACTTTTTAAATTGCAACTGTAA 561 ATATGAAATGGTCATCACATCTGACCTTGGTCAGTGGGGAGGGGAACTGGTATCCTGCCAAGCCTGGTTGTAATTTGTAA 641 CCATTTTCTATTTGTGCAAACTCTGTAAATATGTGTTTAAACAAATGTAATATTTTGTACAAGATACACTGGAGAACAAA 721 GGGAACTCAAGATTCTTCCAGCCACATGTCACCTGTAGGTAGAAGTAAACTCTGCAGTGCAGCTTCTGCTCTTGGCCCCT 801 CTGGCCAGGGCCCCTGTGGCTTCCTGCACACTGGACAGGTGACTGTATGGTAGAGACTGTGATCTGGGAACTTTTTGCTG 881 TACAAATCTGTTTAAAAAAAAAAAAAAGTAACTCATTGAATTAACTTGCAGTGGTGTGTTTGATTCTTTTTTAGACTGGC 961 TTCAGCATTGTGCAGTTTAAAAATAAGTAAGTAACTTACATAAATCTTCAATTGTATGAACTGCA 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 | 8165.0 |
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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 GSM4903833 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
Location of target site | NM_001242903 | 3UTR | GAGUUGAUGAUAUUUAACCAGUUUUUAUAAACUUCAUUUAGGUCUCUAAACACAGACUUUUUAAAUUGCAACUGUAAAUAUGAAAUGGUCAUCACAUCUGACCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 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_001242903 | 3UTR | UAAACACAGACUUUUUAAAUUGCAACUGUAAAUAUGAAAUGGUCAUCACAUCUGACCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 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_001242903 | 3UTR | CUGUAAAUAUGAAAUGGUCAUCACAUCUGACCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 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_001242903 | 3UTR | UUUAAAUUGCAACUGUAAAUAUGAAAUGGUCAUCACAUCUGACCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000337714.3 | 3UTR | UAACCAUUUUCUAUUUGUGCAAACUCUG |
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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88 hsa-miR-4699-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT056239 | RAB18 | RAB18, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT080536 | PMAIP1 | phorbol-12-myristate-13-acetate-induced protein 1 | ![]() |
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2 | 2 | ||||||
MIRT095600 | NR3C1 | nuclear receptor subfamily 3 group C member 1 | ![]() |
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2 | 2 | ||||||
MIRT128911 | KMT2A | lysine methyltransferase 2A | ![]() |
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2 | 2 | ||||||
MIRT161904 | FXR1 | FMR1 autosomal homolog 1 | ![]() |
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2 | 4 | ||||||
MIRT177614 | UBE2D1 | ubiquitin conjugating enzyme E2 D1 | ![]() |
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2 | 4 | ||||||
MIRT231364 | EDEM3 | ER degradation enhancing alpha-mannosidase like protein 3 | ![]() |
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2 | 6 | ||||||
MIRT285164 | SERBP1 | SERPINE1 mRNA binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT307337 | SEC22C | SEC22 homolog C, vesicle trafficking protein | ![]() |
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2 | 2 | ||||||
MIRT317083 | DEK | DEK proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT347692 | LSM14A | LSM14A, mRNA processing body assembly factor | ![]() |
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2 | 2 | ||||||
MIRT358438 | STC2 | stanniocalcin 2 | ![]() |
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2 | 2 | ||||||
MIRT362592 | PURB | purine rich element binding protein B | ![]() |
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2 | 4 | ||||||
MIRT441441 | HAVCR1 | hepatitis A virus cellular receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT445264 | LOH12CR2 | loss of heterozygosity, 12, chromosomal region 2 (non-protein coding) | ![]() |
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2 | 4 | ||||||
MIRT447097 | SNRPD1 | small nuclear ribonucleoprotein D1 polypeptide | ![]() |
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2 | 2 | ||||||
MIRT449013 | ANKRD17 | ankyrin repeat domain 17 | ![]() |
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2 | 2 | ||||||
MIRT450358 | SETD9 | SET domain containing 9 | ![]() |
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2 | 2 | ||||||
MIRT454976 | MYC | MYC proto-oncogene, bHLH transcription factor | ![]() |
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2 | 2 | ||||||
MIRT461922 | NECAB3 | N-terminal EF-hand calcium binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT465191 | TRPS1 | transcriptional repressor GATA binding 1 | ![]() |
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2 | 2 | ||||||
MIRT467685 | SLC38A2 | solute carrier family 38 member 2 | ![]() |
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2 | 4 | ||||||
MIRT468003 | SKI | SKI proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT473127 | MLLT10 | MLLT10, histone lysine methyltransferase DOT1L cofactor | ![]() |
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2 | 2 | ||||||
MIRT476370 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 2 | ||||||
MIRT477067 | FAM208B | family with sequence similarity 208 member B | ![]() |
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2 | 4 | ||||||
MIRT479950 | CBX4 | chromobox 4 | ![]() |
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2 | 4 | ||||||
MIRT481092 | B3GNT2 | UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT481932 | ANKRD11 | ankyrin repeat domain 11 | ![]() |
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2 | 12 | ||||||
MIRT482239 | AHCY | adenosylhomocysteinase | ![]() |
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2 | 2 | ||||||
MIRT485804 | ARPP19 | cAMP regulated phosphoprotein 19 | ![]() |
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2 | 2 | ||||||
MIRT492026 | TWF1 | twinfilin actin binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT494389 | CALM3 | calmodulin 3 | ![]() |
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2 | 2 | ||||||
MIRT504115 | GPR158 | G protein-coupled receptor 158 | ![]() |
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2 | 2 | ||||||
MIRT506346 | NUP54 | nucleoporin 54 | ![]() |
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2 | 4 | ||||||
MIRT510081 | PPWD1 | peptidylprolyl isomerase domain and WD repeat containing 1 | ![]() |
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2 | 4 | ||||||
MIRT521019 | SLC8A1 | solute carrier family 8 member A1 | ![]() |
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2 | 2 | ||||||
MIRT524709 | BTBD3 | BTB domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT524989 | AGO2 | argonaute 2, RISC catalytic component | ![]() |
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2 | 6 | ||||||
MIRT525003 | ACVR1B | activin A receptor type 1B | ![]() |
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2 | 2 | ||||||
MIRT528064 | OLAH | oleoyl-ACP hydrolase | ![]() |
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2 | 2 | ||||||
MIRT528865 | C1orf147 | chromosome 1 open reading frame 147 | ![]() |
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2 | 2 | ||||||
MIRT532182 | DOCK7 | dedicator of cytokinesis 7 | ![]() |
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2 | 2 | ||||||
MIRT533592 | TOB1 | transducer of ERBB2, 1 | ![]() |
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2 | 6 | ||||||
MIRT538835 | C16orf70 | chromosome 16 open reading frame 70 | ![]() |
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2 | 2 | ||||||
MIRT539488 | ACVR1C | activin A receptor type 1C | ![]() |
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2 | 2 | ||||||
MIRT539542 | ABCD2 | ATP binding cassette subfamily D member 2 | ![]() |
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2 | 2 | ||||||
MIRT542123 | VENTX | VENT homeobox | ![]() |
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2 | 2 | ||||||
MIRT542993 | ELOVL5 | ELOVL fatty acid elongase 5 | ![]() |
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2 | 2 | ||||||
MIRT543067 | ATXN7L3B | ataxin 7 like 3B | ![]() |
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2 | 2 | ||||||
MIRT543370 | CYB5B | cytochrome b5 type B | ![]() |
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2 | 2 | ||||||
MIRT545080 | TSEN34 | tRNA splicing endonuclease subunit 34 | ![]() |
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2 | 2 | ||||||
MIRT545258 | TRIM36 | tripartite motif containing 36 | ![]() |
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2 | 4 | ||||||
MIRT549144 | BRIX1 | BRX1, biogenesis of ribosomes | ![]() |
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2 | 2 | ||||||
MIRT549403 | AKAP1 | A-kinase anchoring protein 1 | ![]() |
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2 | 2 | ||||||
MIRT552143 | MRPL34 | mitochondrial ribosomal protein L34 | ![]() |
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2 | 2 | ||||||
MIRT554781 | RHEBP1 | RHEB pseudogene 1 | ![]() |
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2 | 4 | ||||||
MIRT555991 | NFYB | nuclear transcription factor Y subunit beta | ![]() |
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2 | 2 | ||||||
MIRT556425 | LONRF3 | LON peptidase N-terminal domain and ring finger 3 | ![]() |
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2 | 2 | ||||||
MIRT558325 | DNAJC28 | DnaJ heat shock protein family (Hsp40) member C28 | ![]() |
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2 | 4 | ||||||
MIRT561357 | YWHAH | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta | ![]() |
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2 | 2 | ||||||
MIRT562240 | HMGB1 | high mobility group box 1 | ![]() |
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2 | 2 | ||||||
MIRT562269 | GOLT1B | golgi transport 1B | ![]() |
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2 | 2 | ||||||
MIRT564020 | FAM103A1 | family with sequence similarity 103 member A1 | ![]() |
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2 | 2 | ||||||
MIRT564832 | ZBTB16 | zinc finger and BTB domain containing 16 | ![]() |
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2 | 2 | ||||||
MIRT565350 | TMED2 | transmembrane p24 trafficking protein 2 | ![]() |
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2 | 2 | ||||||
MIRT565678 | SET | SET nuclear proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT576547 | Txlna | taxilin alpha | ![]() |
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2 | 2 | ||||||
MIRT609358 | ZNF664 | zinc finger protein 664 | ![]() |
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2 | 2 | ||||||
MIRT610646 | CTGF | connective tissue growth factor | ![]() |
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2 | 2 | ||||||
MIRT624681 | ARAP2 | ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 | ![]() |
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2 | 2 | ||||||
MIRT637118 | AGTPBP1 | ATP/GTP binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT639955 | PRRC2B | proline rich coiled-coil 2B | ![]() |
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2 | 2 | ||||||
MIRT644051 | WWC2 | WW and C2 domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT650463 | SLC35B1 | solute carrier family 35 member B1 | ![]() |
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2 | 2 | ||||||
MIRT651094 | ZNF516 | zinc finger protein 516 | ![]() |
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2 | 2 | ||||||
MIRT655268 | PER2 | period circadian clock 2 | ![]() |
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2 | 2 | ||||||
MIRT657450 | HEYL | hes related family bHLH transcription factor with YRPW motif-like | ![]() |
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2 | 2 | ||||||
MIRT692248 | POLR3F | RNA polymerase III subunit F | ![]() |
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2 | 2 | ||||||
MIRT695239 | PBK | PDZ binding kinase | ![]() |
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2 | 2 | ||||||
MIRT696024 | NDUFS3 | NADH:ubiquinone oxidoreductase core subunit S3 | ![]() |
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2 | 2 | ||||||
MIRT698486 | TIAL1 | TIA1 cytotoxic granule associated RNA binding protein like 1 | ![]() |
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2 | 2 | ||||||
MIRT700581 | PRSS22 | protease, serine 22 | ![]() |
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2 | 2 | ||||||
MIRT704540 | CNEP1R1 | CTD nuclear envelope phosphatase 1 regulatory subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT704723 | CEP135 | centrosomal protein 135 | ![]() |
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2 | 2 | ||||||
MIRT705194 | BTG1 | BTG anti-proliferation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT710286 | CSNK1G3 | casein kinase 1 gamma 3 | ![]() |
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2 | 2 | ||||||
MIRT719623 | TUBGCP3 | tubulin gamma complex associated protein 3 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||
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