pre-miRNA Information | |
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pre-miRNA | hsa-mir-4760 |
Genomic Coordinates | chr21: 40212352 - 40212431 |
Description | Homo sapiens miR-4760 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||
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Mature miRNA | hsa-miR-4760-5p | |||||||||
Sequence | 10| UUUAGAUUGAACAUGAAGUUAG |31 | |||||||||
Evidence | Experimental | |||||||||
Experiments | Illumina | |||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | GTF2E1 | ||||||||||||||||||||
Synonyms | FE, TF2E1, TFIIE-A | ||||||||||||||||||||
Description | general transcription factor IIE subunit 1 | ||||||||||||||||||||
Transcript | NM_005513 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on GTF2E1 | |||||||||||||||||||||
3'UTR of GTF2E1 (miRNA target sites are highlighted) |
>GTF2E1|NM_005513|3'UTR 1 GCTTTCCCTAATTCTTTCTCCTTTCTCTAATGCTCAGTTCAAAAAGGAATGTCTCATCTTTGAAGAAAAGTATTTAAGTG 81 GCTTTCTGCCCCTCTTGATGTAAGCAACTGTCCATCCTTGTGCAAAGATTGATGGTAGAGAGTTTGACTTTTATGCCAGA 161 AACTTTCCCAGCAAGGTAGGGTGCTGAGAATCCTACCCTTCCTTGCTGTCACTACAGTATTAATATTTTACTGTATTTTC 241 TTTTCTTTTTTTTTTTTTTTTGGAGATGAAGTCTCACTCTTGTACCCCAGGCTGGAGTGCAATGGCGTGATCTCGGCTCA 321 CTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGCCTGCCACC 401 ATGCCTGGCTAATTTTTGTATTTTTAGTAGAGGCAGGGTTTCACCATGTTAGCCAGGATGATCTCGATCTCCTGACCTCA 481 TGATCCACCCGCCTCGGCCTCCCAAAGTGCTGTATTTTCTTATCTGATTTTTTTCTTGCCTTATTAAGACATAATTTTCT 561 CCCTTCTGAAATGAGTGAGGGAAGTTCATAAGGTAAATCCTTCCCATCCATCTGTTTACTACAATAGGTTACAATAATTC 641 ACTGATCACATCCATTTTATCTGTTCTAGCCAGGCATTCCAAACAATTTCTTATACTGCTGCCCACCAAAGCAGCTTGCC 721 AACAGTCAAATCACTGATTGGGGGAAAAAATCCTGAAATTTTGCTTAGAATTTGAGCATTTCCTCAAAATTGAGATGGAT 801 CAATATGTAAGGGGAGGTGGGAGCGTGTGTGGAAGGGGGAGAGATATACTTGAGTCTTATGATTAATGTCTAAACCAGAA 881 TTTGTGTCTTTAGAACTGACCAGACTGGTAGATTTTATTGTATTGCTTAATGTCTTTTGGTTTGGATTTAGGATGATAGA 961 AAACAGAAGTATAATTGGTAAACCCTTAGGAAGAAATTAGAAAAACATGGACGTAAGACAAGAAGTCTCTGTGAAGGGTT 1041 GAAGAGTGACAAGCATTGGTAACAGTGCCTTAGAACTGTGTCAGTTAGTCTGATTTGGAAATCCTTTATGTAAAGCTGAG 1121 ACTGGTCCTGGTTTTGTTCCCTTTGGGTACAGACCTCTTGTCAGTGCTATAAATTGTTTAATGAGGCCATTCCAGCAGAA 1201 ATCAACAGAATAATTGATTACTCTTCTCTCTCTCTGTCACTCTCCCTCTTTCTAAACATCATTGAAGGCTGTCTCTCTTT 1281 TAATTTTTGTCAGACACAGTATTTTAGGGTGCATCCAGTATACCATTGAGCATTGTAACCTCAGGAAACAGTTTATTTTG 1361 GGTTCTGATATGTAGCATGGTATTTTCCCTAAGGCAGAACTTTAAAAATAAAGAACTTTCACACAAGGGTCTGTAACAAT 1441 TGTATATCTTACAATATTTTTCCTTGCATTGTAATTTTTAAGTATTTATCATTTTATAGTACACATGTAAAGAATATATG 1521 AGCCTTGTATGGAGTGATGTTTCATTTACCTGGGTTGTGTTAATGACTGAATGTTGACAATAAATCTGTTTTATACTGA 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 | 2960.0 |
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
"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 GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000283875.5 | 3UTR | AUCUAAACUUUUUGUGCAAUAAGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000283875.5 | 3UTR | AUCUAAACUUUUUGUGCAAUAAG |
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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56 hsa-miR-4760-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT076215 | ALKBH5 | alkB homolog 5, RNA demethylase | 2 | 2 | ||||||||
MIRT087763 | H1F0 | H1 histone family member 0 | 2 | 2 | ||||||||
MIRT093991 | SLAIN2 | SLAIN motif family member 2 | 2 | 2 | ||||||||
MIRT109199 | VMA21 | VMA21, vacuolar ATPase assembly factor | 2 | 4 | ||||||||
MIRT243167 | SOX11 | SRY-box 11 | 2 | 2 | ||||||||
MIRT290697 | POLI | DNA polymerase iota | 2 | 2 | ||||||||
MIRT352597 | PTMA | prothymosin, alpha | 2 | 4 | ||||||||
MIRT443107 | DENND5B | DENN domain containing 5B | 2 | 2 | ||||||||
MIRT445651 | ATP6V1G1 | ATPase H+ transporting V1 subunit G1 | 2 | 6 | ||||||||
MIRT449111 | PHEX | phosphate regulating endopeptidase homolog X-linked | 2 | 2 | ||||||||
MIRT449798 | ZNF74 | zinc finger protein 74 | 2 | 2 | ||||||||
MIRT456143 | RWDD2A | RWD domain containing 2A | 2 | 18 | ||||||||
MIRT463303 | ZFP36L1 | ZFP36 ring finger protein like 1 | 2 | 6 | ||||||||
MIRT466904 | STK38 | serine/threonine kinase 38 | 2 | 10 | ||||||||
MIRT492452 | RBPJ | recombination signal binding protein for immunoglobulin kappa J region | 2 | 8 | ||||||||
MIRT511574 | HIST2H3D | histone cluster 2 H3 family member d | 2 | 4 | ||||||||
MIRT519374 | FKBP14 | FK506 binding protein 14 | 2 | 2 | ||||||||
MIRT520935 | SRSF4 | serine and arginine rich splicing factor 4 | 2 | 4 | ||||||||
MIRT524345 | CREB1 | cAMP responsive element binding protein 1 | 2 | 2 | ||||||||
MIRT530230 | WSB2 | WD repeat and SOCS box containing 2 | 2 | 2 | ||||||||
MIRT531864 | POF1B | premature ovarian failure, 1B | 2 | 2 | ||||||||
MIRT534916 | PTPN4 | protein tyrosine phosphatase, non-receptor type 4 | 2 | 2 | ||||||||
MIRT536707 | IKZF2 | IKAROS family zinc finger 2 | 2 | 2 | ||||||||
MIRT543555 | RPF2 | ribosome production factor 2 homolog | 2 | 4 | ||||||||
MIRT545247 | GTF2E1 | general transcription factor IIE subunit 1 | 2 | 2 | ||||||||
MIRT545376 | PM20D2 | peptidase M20 domain containing 2 | 2 | 2 | ||||||||
MIRT548107 | GDAP2 | ganglioside induced differentiation associated protein 2 | 2 | 2 | ||||||||
MIRT548301 | EPHA7 | EPH receptor A7 | 2 | 2 | ||||||||
MIRT551453 | CARKD | NAD(P)HX dehydratase | 2 | 2 | ||||||||
MIRT553195 | UBE2A | ubiquitin conjugating enzyme E2 A | 2 | 2 | ||||||||
MIRT559416 | ASH1L | ASH1 like histone lysine methyltransferase | 2 | 2 | ||||||||
MIRT561360 | YOD1 | YOD1 deubiquitinase | 2 | 2 | ||||||||
MIRT561380 | TWF1 | twinfilin actin binding protein 1 | 2 | 2 | ||||||||
MIRT562062 | KLHL15 | kelch like family member 15 | 2 | 2 | ||||||||
MIRT563482 | ZWINT | ZW10 interacting kinetochore protein | 2 | 2 | ||||||||
MIRT563510 | APOOL | apolipoprotein O like | 2 | 2 | ||||||||
MIRT571391 | MRPL19 | mitochondrial ribosomal protein L19 | 2 | 2 | ||||||||
MIRT573764 | PRKAG1 | protein kinase AMP-activated non-catalytic subunit gamma 1 | 2 | 2 | ||||||||
MIRT576963 | Anxa4 | annexin A4 | 2 | 3 | ||||||||
MIRT611048 | DAB2 | DAB2, clathrin adaptor protein | 2 | 2 | ||||||||
MIRT614297 | ARL6IP6 | ADP ribosylation factor like GTPase 6 interacting protein 6 | 2 | 2 | ||||||||
MIRT619715 | FCF1 | FCF1, rRNA-processing protein | 2 | 2 | ||||||||
MIRT622278 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | 2 | 2 | ||||||||
MIRT622624 | PPM1K | protein phosphatase, Mg2+/Mn2+ dependent 1K | 2 | 2 | ||||||||
MIRT624730 | ANXA4 | annexin A4 | 2 | 3 | ||||||||
MIRT626553 | ZYG11B | zyg-11 family member B, cell cycle regulator | 2 | 2 | ||||||||
MIRT649762 | USP22 | ubiquitin specific peptidase 22 | 2 | 2 | ||||||||
MIRT652063 | TTC39B | tetratricopeptide repeat domain 39B | 2 | 2 | ||||||||
MIRT653045 | STON2 | stonin 2 | 2 | 2 | ||||||||
MIRT660573 | AQR | aquarius intron-binding spliceosomal factor | 2 | 2 | ||||||||
MIRT686243 | ZFR | zinc finger RNA binding protein | 2 | 2 | ||||||||
MIRT703405 | FZD6 | frizzled class receptor 6 | 2 | 2 | ||||||||
MIRT709480 | LOXL2 | lysyl oxidase like 2 | 2 | 2 | ||||||||
MIRT711268 | SDR9C7 | short chain dehydrogenase/reductase family 9C member 7 | 2 | 2 | ||||||||
MIRT711426 | PROSER2 | proline and serine rich 2 | 2 | 2 | ||||||||
MIRT720030 | CDK13 | cyclin dependent kinase 13 | 2 | 2 |