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 | FAM122B | ||||||||||||||||||||
Synonyms | SPACIA2 | ||||||||||||||||||||
Description | family with sequence similarity 122B | ||||||||||||||||||||
Transcript | NM_001166599 | ||||||||||||||||||||
Other Transcripts | NM_001166600 , NM_001170756 , NM_001170757 , NM_145284 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on FAM122B | |||||||||||||||||||||
3'UTR of FAM122B (miRNA target sites are highlighted) |
>FAM122B|NM_001166599|3'UTR 1 CTTAACCATTTCTGATTCAACGTTTTAACTGCTGTTTCCTACATAAAATGTTTAGTGGGGAACGCAGAGAACTTTGATCC 81 ATAATGAGGATTAAAGTTTTACAGATTTCACACATTCTGATGCTATTATTACTCTTTGGCATCTCTCTTCTCCAAAGTTC 161 AATTTTGTGAGCCTAGTGACCTTACTAGTATCTGGTTTTGCTGATCTCATTTTGGATTTAGTGATTAAATCTCAAATGCT 241 GATTTTTGATTGCTTAGAGGAATCTTTTTTCTTAGTGCCTCAAAAAACACCTATTTTGAGTCTATACATTTAAGAAAGGC 321 ACTGATGTGTATTGCCTTTAATGGTCCTTTTCCGCAGCAGTGATATGACAGATTTGATCAGAAATTCTCTTGCTTGAGAG 401 ATTTTTTTTTGTCCTCTGTTGACTACATAGTTTCAAATCTCTCTTTATTTCATGATGATATATAAATTGCTTTTAATTAT 481 ATTAAATTTTTATTTTTCTGCATCAGCTTCAAGTACATTATTTTGTTTCCCTTTCCTGTTTGAGCCGCTTATGCCATTTC 561 TCACAGAGGGGAAGAAATACGTAGTTGCTTTCATTACTCTTATTGCTTCTTTGCTGTTGGGGTGTGTGAAGTGAGCATTG 641 ATTTTAGTGCTGAGAATGTAAACGGACTTACAGGATGCTTGGATTAGTCATCACAGGTTCTTATGACTTTGCTACCACAG 721 TTGATATATTTCTCCTCAAACCTGTTGCCCTAAGGAATATATAAAATATTGTTGATATTTCTAGGTGGTGTTATCAAGGA 801 GAAGAAATTCCTGCCTTGACCAGATGTGTGGAGCATCTACAAATGAATGAATAGTTATTTACACACAAACCACTGTGTAC 881 AAAAGCGTCCATGGAGCTGTCAGTGTCTCGAGTGGTATTATGAGGCCTCAGGTGCCTTGGGGTACATTGTCATGCTATAA 961 GGGATGTATATCATAAGGTATGGTGGAAGAGGGGCCTTATGTGAATGATTGCCACATACTGTTTCTGTTGCTGCTTTTTT 1041 TCCGATTCCTTTTTGTCATTGGATTTGTTTGTTTTGTCATGTGGTGAATGGTGTTTTAGTTATTGTGTTGCTGCCAGAAT 1121 CAGAATCCAGTTCTTGTTCTTACTGCCTTATAGTTATTGTGTTGCCACCAGAATCAGAATCCAGTTCTTGTTCATACTGC 1201 CTTGTAGTGAGGGCAGTTTAATATCTACAAAGAAGCTTTTAGAAGCTGAAAAAGTCAATGTGATTGTGCATTCTGCTTTT 1281 AAGAAGCTGTTTCAGCTATGAACTGTGTATGTGCTATAAGTGTGAGGTACCATAAGTTATTTAATTTTTAAAAGAGGAAA 1361 CTCCTGAGTGAGCTGTTTAAGAAATCTGAGTGTGATCTATTGTTACGTTATTTATAACTAGGTAAAATGTCTGTCGTGAT 1441 AGATTTCTTTTAACGTTCAGATACTGTGGTTGGGTTGTCTATATTTAATATGCAGATTTGCCTGCTGGAATCATAATCCA 1521 TTTTTAAGTGAATGTAAGAAATGAAAACTACTGCATTTGTGTCTTTTGAAGGCAAGGATCCTTGGATTTTAAAGGAAGAG 1601 TATGTGCTTTGAAGGCACTCAGAGACTAGTAATAGCATATGGTTTGAAGGGAAACCCATTCTCTTTCAATTACAAGAGAG 1681 CATCACTTAGCGTGCAGTACTTCTGTTACAGCATCCGATGTGTCCTTTATTTTAAATTGTAACCATAACAGCCATTAATG 1761 GCTTTATTTCTTGTATTGCTCTCATCTGGGAAAAGTCTCTACTTCTTCAAACGTAACATAAATCTATTATGAAGCTTGTC 1841 CCCTAGTATGCCATTATAAAGAAAAAATTCTTCGATGGTATGCAGTGTATCTATTCTGTTTGTAAAAGATCATGTCAAAA 1921 TGTTCTGCCTCTATAATGATAATAGATGGTTTTGTCTTTCAGGATATTTATCCACCTACTGTCTTCTTTGCCTTAAAGGG 2001 ACACTTGGCCATCATTTTTAGGCTCGAACTTAACACTGTTAAGAAATAACTGAAATATGATGGTATTTACATTAATTTTT 2081 GAAATTCAATGGTGGGATAGAATTAGGTCAGGAAATGGAAGTTGTTCCAATGGTGTGAGAACTAGGAGACAAGATGATTC 2161 ACTTTATTATTTAAACCAAGCTTCATTTTTAGTTTTTGTTGTTTAAATGGACTGGAAAGTTAAGTTTTTGCAGGGATTGT 2241 TTTGAAATAAAGAGATATGCTAACTCACAGATGAACTTTGTTAAGACCCCTTTATTTTTATATAAAGTCTAATATTTGAA 2321 AAGCGATTGTTATAAAGTAAAATTCTCTCTTCCTATTCTAATATATATCATATATTTCAGGCTTCTATTTGAAAACAGGT 2401 ATAAGAGATGATATGATACAACCCTATAGATAATGTTTTTTGCTTGATTGACTTATATAATCACTGTTTCATGATTACTG 2481 CTTTTGGAATAATAGGAAGTTTTGTGAAATGCTGGCCTTGTGTATATCTTAGAATGCAAATTTAATAAAGTGTGTATACA 2561 TGCATAAAATTTAAAAAAAAAAA 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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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 | 159090.0 | ||||||
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 | ENST00000370790.1 | 3UTR | CCACAUACUGUUUCUGUUGCUGCUUUUUUUCCGA |
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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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 |