pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-6830 |
Genomic Coordinates | chr5: 132217849 - 132217918 |
Description | Homo sapiens miR-6830 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-6830-3p | ||||||||||||||||||||||||
Sequence | 48| UGUCUUUCUUCUCUCCCUUGCAG |70 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Meta-analysis | ||||||||||||||||||||||||
SNPs in miRNA |
|
||||||||||||||||||||||||
Putative Targets |
Gene Information | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | SNX10 | ||||||||||||||||||||
Synonyms | OPTB8 | ||||||||||||||||||||
Description | sorting nexin 10 | ||||||||||||||||||||
Transcript | NM_013322 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SNX10 | |||||||||||||||||||||
3'UTR of SNX10 (miRNA target sites are highlighted) |
>SNX10|NM_013322|3'UTR 1 AAAATAATTCTAATGTTACTATCTTAGGAATAGCAAATTATGTCCAGTCATAGAGAAGAAAGCTTCATAATAATACATTC 81 TTACCTAAAGCTCACTGTCATGATGTTAGGTATTTAAATTCTTAAAGATGTTGGGTTGTTTATTAGTGGTATTTTTATGT 161 TGTCTTATTTTAGGTAAGCTTCTGTGTAAAGCTAAAAATCCTGTGAATACAATACTATCCTTTACAGGCAGACATTATTG 241 GTAAACAAGATCTTGCCCTCCAATGAAATGACTTACATGTTTTAAAAAACCGAGTTGGTTTTATTGAATTTAAAAAGATA 321 GGTAACTAAGTAGCATTTAAAATCAAGATAGAGCATTCCTTCTTGTATCAGTGGGGCAGTGTTACCATAAACACGGTGTA 401 TATGTTGTTAAACCCTATGAAGAGTAACAGTGTAGACCAGACTGCCTCTCTCAGATATGTGCCTGATATTTTGTGGATAC 481 CTCCCCTGCACTGGCAAAACACTATGCTTTTGGGTGTTAGACTGAAATATTTTAAGAGTATTTAACCTTTCCAGTATTCT 561 GTTTCACGCTTAGATGGAAATGTATCTTATGAATAGAGACATATTAAAATAATGTTTACATCTTAGAAAAAACATAGATA 641 GTGCTAGTAATATTACTTATAACTGTAATATATAGATTCAGAAATACATTTTCATTATCCAAAATCAGCTTCAACAAATG 721 GTTTCTGGAGACAAATAATTTGTTTTCATTATCATTGTATAATCAGGTTAATGATTTATTTTTTGACTAAATGTGCAATT 801 TCTTATCACTAGATAACTTTCAGTATCAGTGGTGGTTACTTATTACTTAAATCAGAGGAAGGATTTTATAAAGATTAATA 881 AATTTAATTTTACCAATAAATATTCCCATAATTTAGAAAAGGATGTCGACTTGCTAATTTCAGAAATAATTATTCATTTT 961 TAAAAAGCCCCTTTTAAAGCATCTACTTGAAGATTGGTATAATTTTCATAAAATGTCTTTTTTTTTAGTGTCCCAAAGAT 1041 ATCTTAGATAAACTATTTTGAAGTTCAGATTTCAGATGAGGCAACATTTTCTTGAGATAATTACCCAAGTTTCATCCATG 1121 TTGAATGGTACAAAATATTTCTGTGAAACTAACAGGAAGATATTTTCAGATAACTAGGATAACTTGTTGCTTTGTTACCC 1201 AGCCTAATTGAAGAGTGGCAGAGGCTACTACAAAAAGCAACCTTTTCATTTTCACTAAGAGTTTAAAAGCTATTGTATTA 1281 TTAAAAAGTCTTTACAATGCTTGTTTCAAAGAACCAACAGAAAAAAAAGCTAAGAAAACTGAGAACTAACATTAAAAAAA 1361 TTAAATTTAGAATAAGAATGATTTCTTTAATTTGTCCTTTTTTTCTTTGGTCTAAAACATTATTAAATTTTTGTAAATAT 1441 TTTGATTTAATGTGTCTTAGATCCTCATTATTTTAATACAGGAAAAGAAAAGATTTAGTAATTTCTTACCATGCTAATAT 1521 GTAAAGTTCATGCCATCCAGGCATTTAAGAGCGATCCTCATCCCTTCAGCAATATGTATTTGAGTTCACACTATTTCTGT 1601 TTTACAGCAGTTTTGAAAAACACATACTATGCCACCAATTGTCATATTATTTTTAGATGATGTAACATAGCCATCAAAAT 1681 TAATATTATGTAATGCCTAATACTTAGTATGTAAATGTCACGAGATCATTTTTACATTAAACGTGAAAAAAAATCAAAAA 1761 AAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
|
||||||||||||||||||||
miRNA-target interactions (Predicted by miRanda) |
|
||||||||||||||||||||
DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
---|---|
miRNA:Target | ---- |
Validation Method |
|
Conditions | HEK293 |
Disease | 29887.0 |
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]
|
CLIP-seq Support 1 for dataset GSM714645 | |
---|---|
Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000396376.1 | 3UTR | CUUCAUAAUAAUACAUUCUUACCUAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
---|---|---|---|---|---|---|---|
|
MiRNA-Target Expression Profile (TCGA) | |||||||
---|---|---|---|---|---|---|---|
|
82 hsa-miR-6830-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT081461 | SSBP4 | single stranded DNA binding protein 4 | 2 | 2 | ||||||||
MIRT132029 | IER5 | immediate early response 5 | 2 | 2 | ||||||||
MIRT187279 | DAZAP2 | DAZ associated protein 2 | 2 | 6 | ||||||||
MIRT350303 | TMEM189-UBE2V1 | TMEM189-UBE2V1 readthrough | 2 | 8 | ||||||||
MIRT350307 | UBE2V1 | ubiquitin conjugating enzyme E2 V1 | 2 | 8 | ||||||||
MIRT372105 | EIF3H | eukaryotic translation initiation factor 3 subunit H | 2 | 2 | ||||||||
MIRT408159 | DCK | deoxycytidine kinase | 2 | 4 | ||||||||
MIRT442623 | LOX | lysyl oxidase | 2 | 2 | ||||||||
MIRT442952 | ASXL2 | additional sex combs like 2, transcriptional regulator | 2 | 2 | ||||||||
MIRT469401 | REL | REL proto-oncogene, NF-kB subunit | 2 | 6 | ||||||||
MIRT476631 | G2E3 | G2/M-phase specific E3 ubiquitin protein ligase | 2 | 2 | ||||||||
MIRT485039 | TMEM189 | transmembrane protein 189 | 2 | 8 | ||||||||
MIRT485133 | RASSF8 | Ras association domain family member 8 | 2 | 6 | ||||||||
MIRT498963 | ORC4 | origin recognition complex subunit 4 | 2 | 8 | ||||||||
MIRT500082 | L2HGDH | L-2-hydroxyglutarate dehydrogenase | 2 | 8 | ||||||||
MIRT503018 | CAND1 | cullin associated and neddylation dissociated 1 | 2 | 2 | ||||||||
MIRT503374 | SCAMP1 | secretory carrier membrane protein 1 | 2 | 2 | ||||||||
MIRT504975 | ZNF711 | zinc finger protein 711 | 2 | 2 | ||||||||
MIRT518984 | NNT | nicotinamide nucleotide transhydrogenase | 2 | 4 | ||||||||
MIRT520754 | TFDP1 | transcription factor Dp-1 | 2 | 6 | ||||||||
MIRT526785 | SGCD | sarcoglycan delta | 2 | 2 | ||||||||
MIRT533868 | TBL1XR1 | transducin beta like 1 X-linked receptor 1 | 2 | 2 | ||||||||
MIRT535107 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | 2 | 2 | ||||||||
MIRT538991 | BAG4 | BCL2 associated athanogene 4 | 2 | 2 | ||||||||
MIRT543518 | PRSS21 | protease, serine 21 | 2 | 2 | ||||||||
MIRT543813 | SNX10 | sorting nexin 10 | 2 | 2 | ||||||||
MIRT543825 | GSG1 | germ cell associated 1 | 2 | 2 | ||||||||
MIRT545334 | CCDC83 | coiled-coil domain containing 83 | 2 | 2 | ||||||||
MIRT545669 | DECR1 | 2,4-dienoyl-CoA reductase 1 | 2 | 2 | ||||||||
MIRT547798 | KAT7 | lysine acetyltransferase 7 | 2 | 2 | ||||||||
MIRT548068 | GIGYF1 | GRB10 interacting GYF protein 1 | 2 | 2 | ||||||||
MIRT549577 | ZNF850 | zinc finger protein 850 | 2 | 2 | ||||||||
MIRT550753 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | 2 | 2 | ||||||||
MIRT550808 | FAM229B | family with sequence similarity 229 member B | 2 | 2 | ||||||||
MIRT551457 | CARKD | NAD(P)HX dehydratase | 2 | 2 | ||||||||
MIRT551852 | RPS3 | ribosomal protein S3 | 2 | 2 | ||||||||
MIRT554218 | SLC30A1 | solute carrier family 30 member 1 | 2 | 2 | ||||||||
MIRT556588 | LEPROT | leptin receptor overlapping transcript | 2 | 2 | ||||||||
MIRT557344 | HDGF | heparin binding growth factor | 2 | 4 | ||||||||
MIRT571945 | LARP1 | La ribonucleoprotein domain family member 1 | 2 | 2 | ||||||||
MIRT574374 | YY1 | YY1 transcription factor | 2 | 2 | ||||||||
MIRT611142 | CRISP1 | cysteine rich secretory protein 1 | 2 | 4 | ||||||||
MIRT611799 | FCRL4 | Fc receptor like 4 | 2 | 2 | ||||||||
MIRT612834 | KCNN3 | potassium calcium-activated channel subfamily N member 3 | 2 | 2 | ||||||||
MIRT617257 | GLIPR1L2 | GLI pathogenesis related 1 like 2 | 2 | 2 | ||||||||
MIRT619781 | NRIP2 | nuclear receptor interacting protein 2 | 2 | 2 | ||||||||
MIRT620440 | SEMA3E | semaphorin 3E | 2 | 2 | ||||||||
MIRT621725 | TNR | tenascin R | 2 | 2 | ||||||||
MIRT622905 | PCDH17 | protocadherin 17 | 2 | 2 | ||||||||
MIRT623428 | KLF6 | Kruppel like factor 6 | 2 | 2 | ||||||||
MIRT627856 | PITPNM3 | PITPNM family member 3 | 2 | 2 | ||||||||
MIRT633894 | FGF10 | fibroblast growth factor 10 | 2 | 2 | ||||||||
MIRT636257 | SEC24D | SEC24 homolog D, COPII coat complex component | 2 | 2 | ||||||||
MIRT640654 | FRY | FRY microtubule binding protein | 2 | 2 | ||||||||
MIRT640857 | TSHZ2 | teashirt zinc finger homeobox 2 | 2 | 4 | ||||||||
MIRT641220 | LRCH1 | leucine rich repeats and calponin homology domain containing 1 | 2 | 2 | ||||||||
MIRT642526 | ANKRD9 | ankyrin repeat domain 9 | 2 | 2 | ||||||||
MIRT646011 | TNFAIP8L2 | TNF alpha induced protein 8 like 2 | 2 | 2 | ||||||||
MIRT653317 | SMOC1 | SPARC related modular calcium binding 1 | 2 | 2 | ||||||||
MIRT657940 | GATM | glycine amidinotransferase | 2 | 2 | ||||||||
MIRT658291 | FAM83F | family with sequence similarity 83 member F | 2 | 2 | ||||||||
MIRT660607 | ANTXR2 | anthrax toxin receptor 2 | 2 | 2 | ||||||||
MIRT664675 | LMBR1L | limb development membrane protein 1 like | 2 | 2 | ||||||||
MIRT664889 | PRRG4 | proline rich and Gla domain 4 | 2 | 2 | ||||||||
MIRT666972 | PHF20L1 | PHD finger protein 20 like 1 | 2 | 2 | ||||||||
MIRT669128 | CD200 | CD200 molecule | 2 | 2 | ||||||||
MIRT673267 | RUNDC1 | RUN domain containing 1 | 2 | 2 | ||||||||
MIRT704609 | CLN8 | CLN8, transmembrane ER and ERGIC protein | 2 | 2 | ||||||||
MIRT709404 | TADA2A | transcriptional adaptor 2A | 2 | 2 | ||||||||
MIRT710963 | CMKLR1 | chemerin chemokine-like receptor 1 | 2 | 2 | ||||||||
MIRT711745 | DTX1 | deltex E3 ubiquitin ligase 1 | 2 | 2 | ||||||||
MIRT715009 | CYP1B1 | cytochrome P450 family 1 subfamily B member 1 | 2 | 2 | ||||||||
MIRT715467 | NEGR1 | neuronal growth regulator 1 | 2 | 2 | ||||||||
MIRT715737 | CD226 | CD226 molecule | 2 | 2 | ||||||||
MIRT716526 | KSR2 | kinase suppressor of ras 2 | 2 | 2 | ||||||||
MIRT718311 | TMPRSS11B | transmembrane protease, serine 11B | 2 | 2 | ||||||||
MIRT719006 | TMEM184C | transmembrane protein 184C | 2 | 2 | ||||||||
MIRT719319 | STAC | SH3 and cysteine rich domain | 2 | 2 | ||||||||
MIRT722092 | SUSD1 | sushi domain containing 1 | 2 | 2 | ||||||||
MIRT723198 | TNRC6C | trinucleotide repeat containing 6C | 2 | 2 | ||||||||
MIRT723239 | BTLA | B and T lymphocyte associated | 2 | 2 | ||||||||
MIRT724850 | IGFBP5 | insulin like growth factor binding protein 5 | 2 | 2 |