pre-miRNA Information | |
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pre-miRNA | hsa-mir-4491 |
Genomic Coordinates | chr11: 111347757 - 111347824 |
Description | Homo sapiens miR-4491 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4491 | ||||||||||||||||||||||||
Sequence | 46| AAUGUGGACUGGUGUGACCAAA |67 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | RBM22 | ||||||||||||||||||||
Synonyms | Cwc2, ZC3H16, fSAP47 | ||||||||||||||||||||
Description | RNA binding motif protein 22 | ||||||||||||||||||||
Transcript | NM_018047 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on RBM22 | |||||||||||||||||||||
3'UTR of RBM22 (miRNA target sites are highlighted) |
>RBM22|NM_018047|3'UTR 1 CACCTTGTCACCACTCTGGGGCTCTGTGGAAGAAAGGGCACTTAAAACTCCCAGTAAATCTTGGAATAAATATATTTTTC 81 CTTCCCTTGTAGTTTCCATGGTAGCTGAATGTGCTCAGATGTGAGCAGTCAGAGACTGACAGCCATGCTTTCCTATACTT 161 GTTCAAAGGATCGATGGACCGTAAATAAGCTGCCATTAACACATCTGGTTACTGCTGTAACATGACTAATAAAACCGAAC 241 GCCTGTTCCCCTTACCCGTGTGGGGGACACGCAGATGAGTGAATTGGAATGTCCAGCAGAGTTACCCTCCCAATTATATG 321 TTCATTTTGTATATTTTTTGGTCGGGGGAAAAATTGACCTGCAGTAAAAAAACCTTTGACCATTTTTATGTCCATTGGAT 401 ACTTTCCTTTTTATCATCTTAAAAAAAGATAACTAGTACTAATCATTGTAGTGGCCTAAGTGTGATTTAACTCTTGAAGT 481 CACACCCTCCGAAAGATGAGTAGAAACCAGCACCAGCACAGCCCAGATCTTCTCTTTCCTCTCCTTTTCCTCATTTATTC 561 CTAAAGGAATCTGACCATTTTACGTCTCTACGGCCCAAAAAAAGACAAAAATAAAAATTCCTTTTTATTCCTGTCAACTG 641 GATGGAAACACAAATTTCATGGAGCTGTGTACCATCGAAGAAACCTGGTGTCTGGCATGAAATTACTGTAAAGAACTTCC 721 TGTAAAACACGTTCTTTAACAAACTGAAATGAAAAGCATTGGAGCGTCTGAATGAAAGACGTGACCTCCTGCTGGGACTC 801 TGATGGTCTTCAGCATTCACCTTCGTGTGTCTTCAGTGTCTCATTGTCATCCCTGCTTCTGTTTGGTCTTAGAGTGTTTG 881 GATATAACTGAATTGTAGATGGTAAAGGAAATTTGATGTGTTTTTTGTTTTTAAATAATTAAAACGGGTCAATTTTTCAC 961 AAAAAAA 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 | 55696.0 |
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. |
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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Experimental Support 2 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293 | ||||||
Disease | 55696.0 | ||||||
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine
... - Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Memczak S; Jens M; Elefsinioti A; Torti F; et al. - Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
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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 | ENST00000199814.4 | 3UTR | AUACACAUACAUACAUACAUAUAUG |
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 GSM1065667 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
Location of target site | ENST00000199814.4 | 3UTR | ACAUCUCCACAUACACAUACAUACAUACAUAUAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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67 hsa-miR-4491 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT056779 | ARID5B | AT-rich interaction domain 5B | ![]() |
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2 | 2 | ||||||
MIRT061577 | BTG2 | BTG anti-proliferation factor 2 | ![]() |
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2 | 2 | ||||||
MIRT063828 | SRP9 | signal recognition particle 9 | ![]() |
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2 | 4 | ||||||
MIRT102306 | DNAJB9 | DnaJ heat shock protein family (Hsp40) member B9 | ![]() |
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2 | 10 | ||||||
MIRT186634 | COX20 | COX20, cytochrome c oxidase assembly factor | ![]() |
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2 | 8 | ||||||
MIRT191243 | STYX | serine/threonine/tyrosine interacting protein | ![]() |
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2 | 2 | ||||||
MIRT195908 | SRSF11 | serine and arginine rich splicing factor 11 | ![]() |
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2 | 4 | ||||||
MIRT240343 | UBXN2B | UBX domain protein 2B | ![]() |
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2 | 2 | ||||||
MIRT271178 | PTPN14 | protein tyrosine phosphatase, non-receptor type 14 | ![]() |
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2 | 2 | ||||||
MIRT286219 | TMEM97 | transmembrane protein 97 | ![]() |
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2 | 4 | ||||||
MIRT314182 | OCLN | occludin | ![]() |
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2 | 4 | ||||||
MIRT323938 | AKAP2 | A-kinase anchoring protein 2 | ![]() |
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2 | 4 | ||||||
MIRT323940 | PALM2-AKAP2 | PALM2-AKAP2 readthrough | ![]() |
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2 | 4 | ||||||
MIRT340113 | TXLNA | taxilin alpha | ![]() |
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2 | 2 | ||||||
MIRT450333 | LRWD1 | leucine rich repeats and WD repeat domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT451283 | ZNF101 | zinc finger protein 101 | ![]() |
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2 | 2 | ||||||
MIRT451879 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 8 | ||||||
MIRT453577 | CRCP | CGRP receptor component | ![]() |
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2 | 2 | ||||||
MIRT454366 | ASAH2 | N-acylsphingosine amidohydrolase 2 | ![]() |
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2 | 2 | ||||||
MIRT454797 | STOML3 | stomatin like 3 | ![]() |
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2 | 2 | ||||||
MIRT459801 | POTED | POTE ankyrin domain family member D | ![]() |
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2 | 10 | ||||||
MIRT460911 | POLQ | DNA polymerase theta | ![]() |
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2 | 2 | ||||||
MIRT468082 | SHOC2 | SHOC2, leucine rich repeat scaffold protein | ![]() |
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2 | 6 | ||||||
MIRT470281 | PRKAA1 | protein kinase AMP-activated catalytic subunit alpha 1 | ![]() |
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2 | 2 | ||||||
MIRT471876 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT476147 | GPR137C | G protein-coupled receptor 137C | ![]() |
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2 | 8 | ||||||
MIRT478056 | DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | ![]() |
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2 | 10 | ||||||
MIRT501054 | SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | ![]() |
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2 | 4 | ||||||
MIRT501732 | OVOL1 | ovo like transcriptional repressor 1 | ![]() |
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2 | 2 | ||||||
MIRT502214 | HSPB8 | heat shock protein family B (small) member 8 | ![]() |
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2 | 2 | ||||||
MIRT505243 | UBE2D3 | ubiquitin conjugating enzyme E2 D3 | ![]() |
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2 | 2 | ||||||
MIRT505957 | RAN | RAN, member RAS oncogene family | ![]() |
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2 | 6 | ||||||
MIRT507996 | BCL2L13 | BCL2 like 13 | ![]() |
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2 | 4 | ||||||
MIRT510433 | ZNF207 | zinc finger protein 207 | ![]() |
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2 | 6 | ||||||
MIRT510827 | SBNO1 | strawberry notch homolog 1 | ![]() |
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2 | 4 | ||||||
MIRT511493 | HNRNPA0 | heterogeneous nuclear ribonucleoprotein A0 | ![]() |
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2 | 4 | ||||||
MIRT512129 | CREBL2 | cAMP responsive element binding protein like 2 | ![]() |
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2 | 8 | ||||||
MIRT514512 | SHISA9 | shisa family member 9 | ![]() |
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2 | 4 | ||||||
MIRT516482 | RAB32 | RAB32, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT519514 | RBM22 | RNA binding motif protein 22 | ![]() |
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2 | 4 | ||||||
MIRT523367 | GTF2A1 | general transcription factor IIA subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT524217 | DDI2 | DNA damage inducible 1 homolog 2 | ![]() |
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2 | 6 | ||||||
MIRT524649 | C4orf32 | family with sequence similarity 241 member A | ![]() |
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2 | 2 | ||||||
MIRT528297 | ZNF76 | zinc finger protein 76 | ![]() |
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2 | 2 | ||||||
MIRT528577 | ITGB3BP | integrin subunit beta 3 binding protein | ![]() |
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2 | 2 | ||||||
MIRT530458 | SULT1B1 | sulfotransferase family 1B member 1 | ![]() |
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2 | 2 | ||||||
MIRT535774 | MYCN | MYCN proto-oncogene, bHLH transcription factor | ![]() |
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2 | 2 | ||||||
MIRT544239 | CCBL2 | kynurenine aminotransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT546733 | RNF217 | ring finger protein 217 | ![]() |
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2 | 2 | ||||||
MIRT550360 | INCENP | inner centromere protein | ![]() |
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2 | 4 | ||||||
MIRT553343 | TRPC3 | transient receptor potential cation channel subfamily C member 3 | ![]() |
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2 | 4 | ||||||
MIRT556629 | LAPTM4A | lysosomal protein transmembrane 4 alpha | ![]() |
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2 | 2 | ||||||
MIRT558006 | FAM122B | family with sequence similarity 122B | ![]() |
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2 | 2 | ||||||
MIRT558994 | CA8 | carbonic anhydrase 8 | ![]() |
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2 | 2 | ||||||
MIRT560418 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | ![]() |
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2 | 2 | ||||||
MIRT565717 | SESN3 | sestrin 3 | ![]() |
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2 | 2 | ||||||
MIRT566271 | PTAR1 | protein prenyltransferase alpha subunit repeat containing 1 | ![]() |
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2 | 2 | ||||||
MIRT568161 | CCDC6 | coiled-coil domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT569753 | C2orf71 | chromosome 2 open reading frame 71 | ![]() |
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2 | 2 | ||||||
MIRT573959 | FIGNL1 | fidgetin like 1 | ![]() |
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2 | 2 | ||||||
MIRT574530 | PEG10 | paternally expressed 10 | ![]() |
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2 | 2 | ||||||
MIRT609453 | CCDC149 | coiled-coil domain containing 149 | ![]() |
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2 | 2 | ||||||
MIRT614047 | THBS2 | thrombospondin 2 | ![]() |
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2 | 2 | ||||||
MIRT628418 | ATMIN | ATM interactor | ![]() |
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2 | 2 | ||||||
MIRT689556 | XPO6 | exportin 6 | ![]() |
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2 | 2 | ||||||
MIRT725598 | CDH7 | cadherin 7 | ![]() |
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2 | 2 | ||||||
MIRT735561 | TRIM7 | tripartite motif containing 7 | ![]() |
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3 | 0 |