pre-miRNA Information | |
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pre-miRNA | hsa-mir-4763 |
Genomic Coordinates | chr22: 46113566 - 46113657 |
Description | Homo sapiens miR-4763 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4763-5p | |||||||||||||||||||||||||||||||||
Sequence | 19| CGCCUGCCCAGCCCUCCUGCU |39 | |||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||
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 | KLHL9 | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | kelch like family member 9 | ||||||||||||||||||||
Transcript | NM_018847 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on KLHL9 | |||||||||||||||||||||
3'UTR of KLHL9 (miRNA target sites are highlighted) |
>KLHL9|NM_018847|3'UTR 1 GTCTAAGGTGTAACACCTTTGCAGTACGTCATGGGTGATCTAATACTTCCCCTTCAGTTGTATCTTCTTACAGTGATTGG 81 TACAGTTATTAGATATAAAGGTAACTGATGTTATTCGTCTTGTATGGCTTTTAGTATGTTTATCAAGTGGCTAACAAATG 161 CATTCTGAAAATGTATTTAACATAGCTGTTTTAACAAATGAAAAAAAGACGTAGAAAAATGTTTAGATGTCTTTTTGTGA 241 TGTTATATAAAATTGTAGATGACTGTGGTAAATGTGTAATTATGTCCATTATGCTTCAAAGTTGAGTTTTCATCTTTGAC 321 TCCAAAATGTCAGAGGGAGGCCGCTCTAAACTAAAAATAACGAAAGGTTGCCAAGTATTAATACTAGTTACCTCCCTCTT 401 TTCGTAGTTTTTGTCATGTCTGTCAACTTACTCGATTGTGTGGTTGCATTCAGAATATTTGAAGTTTCTTACGTAGACAG 481 AAATAATAAAAATATTAACTAGGAAAAAACAGTATAGCACCAAGCCAGTATTTGGTATCTCTCTCTAGAGCGAGCAAGAG 561 AGGGAGAGAGGAGGAAAAAATACACATAATACAAACATACATGCATGCACACATACATACATATGTATACACACACATAA 641 TTTGAAAACTGATTGGCACTTCAACGATGCTGAAATTGTTTTTAAATTGAAGTTTCTTTCTTCCACAAAGCAGCCGTTTC 721 TATTCAAATGGAAATTCAGTACCAGAGAATAAATGTCTATGTAGTCATACTGAATTTAGATAGATAAGGGCTACAGCATA 801 CTAAATCGACAACCAAATTTGTCATGTGACTAAACCGTTACTTCAGATGAAGCTTACATTACTGTTTTCTGCTTGTGTAT 881 TTTCTGTAGAGTACTTTTACACAGATTGGTAAAGTTCAGGTTTCAGAGAACTGCTTTTGTGCAGAAAATTTAGGTTCTTT 961 TTTCCACCTTTTTGGTCAGTAAAACTTAATGAAAAAAGCAAAGAAAAAAATATTCTGAACAAAGCTATAGGGTTTTAAGT 1041 TCAGCCTCCCAACTTAGTCATCCTAACATGATTATTTTGTGATTTGGGGTGCTTGCCCTGGTGCTGTTCCAGTCCATGTG 1121 CATCCTGAGCTGTGTGATCTGCCTCGAGGCTATGATCTGAGCAAGCAGGAGATAACATTTTCTTCTGCATCAAGTGAGGA 1201 AAAATGTGCTTTTGGCCATGTCTCAAAGACAGGACCAACTTCAGATTCCCAAAGAAGCCAGCTACAGAGCCTCTGGAACA 1281 CTATGGTCTTACAAGCAGTACTAAAATCAACCCTCAGCCTCTTCAATGCCAAAGGTATCCCTATTGGTTGAGAACCACAT 1361 GGTAATTTTTAATGGGACTTTTATCAGCAAATGGAGTTACAGGAATTCTCTGTAATGAGTGATTCTGAAGAGGTACTTTC 1441 CTGGAATAATTGTCTACCTGAAGAAAAAAAATTTATATATACATTGTGTGTGTGTGTAATACACACACACAACCCCCTAT 1521 ACCTGGAAGATTGTCAGCATGTAAATCAGGAACAACTTTCTCCTTATTGACAATCCCATAATAAAACTCAGGAACCAAGG 1601 CAAAATGAATTGGCTTCTAGGGGTCTGAACCTTACTGCCCATACAAGTGTTGATTCATTTTAATGCTGTTTATGATTTCT 1681 GCATTGGCAGAAATTTTCATACTTTCTATGTTTTTTTAATTACTCAGTTTTTTATTACTAAAAATAGCACATTTGAGTAC 1761 ATTTGAAAAGTAGAAAAATTAGAAATTATTAACTTTATTGAATAAGCAAGAAGTGCATCCTAATCCTTTGATTATTAATG 1841 AGGTTGAATATTTGTGTGCTATCGGTAGCTGTGTTTCTTTGATCAGATGTTCCTGTCCTTTTGCCCTTCTGTTATCTGTT 1921 GGAGTTGCTTTGTTTTTCGTATCAAGTTATAGGATCTCTTTATATAATAAATGTAATTTAACTTGCATTTGCTTGCATTT 2001 ATTTCTTCCCTCAATCTGTTGTAGTTTTACAAAGGCAACGCTGTTCAGTTAATTTTTGAGATCAAATTTGTCTTTTTTTT 2081 TTTTTGAGACAGGGTCTCACTGTTGTGCAGTCTGGAGTGCAATGGCACGATGTGTGCTCACTGAAACCTCTGCCTCTCAT 2161 GTTCAGGCGATTCTCCCACCTCAGCCTCCCGATTAGCTGGGATTACAGGCATGTACCACCAAGCCCGGCTAATTTTGTAT 2241 TTTTAGTAGAGATGGGGTTAGGGGATAATTTTGATATGGTTTATTTTTTATGTAGTATTTCAGTGCTTATTCTGACATAT 2321 CAAGGTGATACTGCCCTGCCTCTATTTTGTACAGGCTTTTCCTTTTATTGAAAAAAAGTACTTTTTATTACATCTTATGT 2401 CTGAACCTGGTGCTTCCTATTGAAATAAGTATTGCTTTACTAGGTAAACTGCTCTATCTACATCCCCCACCTCCAGCTTC 2481 ACCCACCCTGCCTCTCATTTTTTTACTTTCCCGTATTCTGCAGTTGACAGTTCTCTTGGTAATCATACAGGTAGCTGACT 2561 AATGCTATGCTAATACAGGTTGAGCAGCCCTAATCCAAAAATCCAAATTGCTCCAAAATTTAAAACTTTTTGAGGGCCAA 2641 CAGGATGCCACAAGTAGAAAATTCCACACCAGAGCTCATGTGACAGGTTACACTCAAAACACAGTGAAGACTTGTTTCAT 2721 GCACAACATTATTAAGACTATTATAATTACCTTCAGACTACGTGTCTGAAACGTGAAATATAACCGAAGTTTTAAGTAAT 2801 ATTGTTTAGACTTGGGTCCCTCCCCCAGGATACGTCATGTACATGCAAATATTCCAAAATCCAAAACACTTCTGGTCCCA 2881 AGCATTTCAGATAAGGGATATTCAATCTGTACTGCTCATTAAACCTGGAGTTTCTTATAGAGAGAAATTTTAGGTGGTTG 2961 AAATGATTAAATGGAAAGAGATTTATTTTCATAAGCTGGTAATTTTTTAAAGAAAGTTCAGACTGGAAAAATATTTAGAG 3041 GATAAAAACTAAAAGCACATAAAGCATTATGTTAACATTTCTTGTTTTAGTTTTTCGGAAAGTATTCAAAAATTAACATT 3121 TGTTAGCTTTTTTGATATGTCTATTATAGAACGTACAGGAAAATAAAAGCAAACTAATTTATCAGTGATTCCACATGTTG 3201 AAGATAATTTCTATTAATAGTATATTATATATATATATATACGTACATATGTGCAGGCATTTGTCAAATATTTTTCAAGT 3281 ATGCCAGACCTTAGGCTAAAAGCTGGATAATGAAAATAAATCCACCTTCCAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA 3361 AAAAAAAAAAAAAAA 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 | 55958.0 |
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 | 55958.0 |
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. |
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 | ENST00000359039.4 | 3UTR | UAUAUAUAUAUAUAUACGUACAUAUGUG |
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 | ENST00000359039.4 | 3UTR | UAUAUAUAUAUAUAUACGUACAUAUGUG |
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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69 hsa-miR-4763-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT116035 | DEPDC1 | DEP domain containing 1 | 2 | 2 | ||||||||
MIRT347197 | SIN3B | SIN3 transcription regulator family member B | 2 | 2 | ||||||||
MIRT443248 | C9orf170 | chromosome 9 open reading frame 170 | 2 | 2 | ||||||||
MIRT475164 | IP6K1 | inositol hexakisphosphate kinase 1 | 2 | 2 | ||||||||
MIRT495486 | VTI1B | vesicle transport through interaction with t-SNAREs 1B | 2 | 2 | ||||||||
MIRT496755 | TGIF2 | TGFB induced factor homeobox 2 | 2 | 2 | ||||||||
MIRT496863 | C21orf2 | chromosome 21 open reading frame 2 | 2 | 2 | ||||||||
MIRT499264 | NBPF11 | NBPF member 11 | 2 | 2 | ||||||||
MIRT499517 | MAFK | MAF bZIP transcription factor K | 2 | 2 | ||||||||
MIRT512952 | MKI67 | marker of proliferation Ki-67 | 2 | 2 | ||||||||
MIRT514656 | NUP93 | nucleoporin 93 | 2 | 2 | ||||||||
MIRT517986 | SLC16A13 | solute carrier family 16 member 13 | 2 | 2 | ||||||||
MIRT522816 | KLHL9 | kelch like family member 9 | 2 | 4 | ||||||||
MIRT525495 | CD63 | CD63 molecule | 2 | 2 | ||||||||
MIRT528111 | FOXH1 | forkhead box H1 | 2 | 2 | ||||||||
MIRT531683 | MYO3A | myosin IIIA | 2 | 2 | ||||||||
MIRT534806 | RAB37 | RAB37, member RAS oncogene family | 2 | 2 | ||||||||
MIRT573041 | SHMT1 | serine hydroxymethyltransferase 1 | 2 | 2 | ||||||||
MIRT576720 | Wars | tryptophanyl-tRNA synthetase | 2 | 2 | ||||||||
MIRT609727 | MLXIPL | MLX interacting protein like | 2 | 2 | ||||||||
MIRT610843 | FAM180B | family with sequence similarity 180 member B | 2 | 4 | ||||||||
MIRT614735 | STAT5A | signal transducer and activator of transcription 5A | 2 | 2 | ||||||||
MIRT616981 | EPOR | erythropoietin receptor | 2 | 2 | ||||||||
MIRT617265 | MMAB | methylmalonic aciduria (cobalamin deficiency) cblB type | 2 | 2 | ||||||||
MIRT619405 | INTS7 | integrator complex subunit 7 | 2 | 2 | ||||||||
MIRT621832 | TIMM8A | translocase of inner mitochondrial membrane 8A | 2 | 2 | ||||||||
MIRT621893 | TAF13 | TATA-box binding protein associated factor 13 | 2 | 2 | ||||||||
MIRT630263 | SMIM14 | small integral membrane protein 14 | 2 | 2 | ||||||||
MIRT634879 | SENP8 | SUMO/sentrin peptidase family member, NEDD8 specific | 2 | 2 | ||||||||
MIRT636863 | ARSE | arylsulfatase E (chondrodysplasia punctata 1) | 2 | 2 | ||||||||
MIRT637653 | ADAT1 | adenosine deaminase, tRNA specific 1 | 2 | 2 | ||||||||
MIRT637699 | ZNF439 | zinc finger protein 439 | 2 | 2 | ||||||||
MIRT637759 | GATAD1 | GATA zinc finger domain containing 1 | 2 | 2 | ||||||||
MIRT638193 | TAOK1 | TAO kinase 1 | 2 | 2 | ||||||||
MIRT638996 | ADO | 2-aminoethanethiol dioxygenase | 2 | 2 | ||||||||
MIRT642221 | RABAC1 | Rab acceptor 1 | 2 | 2 | ||||||||
MIRT643327 | ATCAY | ATCAY, caytaxin | 2 | 4 | ||||||||
MIRT643419 | ERVMER34-1 | endogenous retrovirus group MER34 member 1, envelope | 2 | 2 | ||||||||
MIRT644499 | RNF14 | ring finger protein 14 | 2 | 2 | ||||||||
MIRT644603 | NT5DC3 | 5'-nucleotidase domain containing 3 | 2 | 2 | ||||||||
MIRT644795 | C21orf59 | chromosome 21 open reading frame 59 | 2 | 2 | ||||||||
MIRT648732 | HIST1H2BD | histone cluster 1 H2B family member d | 2 | 2 | ||||||||
MIRT653856 | SHE | Src homology 2 domain containing E | 2 | 2 | ||||||||
MIRT654129 | RPL14 | ribosomal protein L14 | 2 | 4 | ||||||||
MIRT658876 | DSN1 | DSN1 homolog, MIS12 kinetochore complex component | 2 | 2 | ||||||||
MIRT671624 | C20orf144 | chromosome 20 open reading frame 144 | 2 | 4 | ||||||||
MIRT677367 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | 2 | 2 | ||||||||
MIRT677579 | TRIM65 | tripartite motif containing 65 | 2 | 2 | ||||||||
MIRT678220 | MACC1 | MACC1, MET transcriptional regulator | 2 | 2 | ||||||||
MIRT679613 | RRP36 | ribosomal RNA processing 36 | 2 | 2 | ||||||||
MIRT686081 | PNPLA3 | patatin like phospholipase domain containing 3 | 2 | 2 | ||||||||
MIRT691817 | ICA1L | islet cell autoantigen 1 like | 2 | 2 | ||||||||
MIRT693869 | COX19 | COX19, cytochrome c oxidase assembly factor | 2 | 2 | ||||||||
MIRT694544 | BPNT1 | 3'(2'), 5'-bisphosphate nucleotidase 1 | 2 | 2 | ||||||||
MIRT694926 | ANKS4B | ankyrin repeat and sterile alpha motif domain containing 4B | 2 | 2 | ||||||||
MIRT697758 | USP37 | ubiquitin specific peptidase 37 | 2 | 2 | ||||||||
MIRT697891 | UBE2B | ubiquitin conjugating enzyme E2 B | 2 | 2 | ||||||||
MIRT701569 | MYPN | myopalladin | 2 | 2 | ||||||||
MIRT703081 | GPRIN3 | GPRIN family member 3 | 2 | 2 | ||||||||
MIRT708104 | IGF2BP1 | insulin like growth factor 2 mRNA binding protein 1 | 2 | 2 | ||||||||
MIRT708320 | NT5C | 5', 3'-nucleotidase, cytosolic | 2 | 2 | ||||||||
MIRT709878 | TRAF1 | TNF receptor associated factor 1 | 2 | 2 | ||||||||
MIRT713545 | GJB1 | gap junction protein beta 1 | 2 | 2 | ||||||||
MIRT716275 | NUP85 | nucleoporin 85 | 2 | 2 | ||||||||
MIRT716621 | CRCP | CGRP receptor component | 2 | 2 | ||||||||
MIRT717987 | C9orf171 | cilia and flagella associated protein 77 | 2 | 2 | ||||||||
MIRT718438 | RAB11B | RAB11B, member RAS oncogene family | 2 | 2 | ||||||||
MIRT722544 | AGPAT4 | 1-acylglycerol-3-phosphate O-acyltransferase 4 | 2 | 2 | ||||||||
MIRT724013 | F2RL1 | F2R like trypsin receptor 1 | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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