pre-miRNA Information | |
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pre-miRNA | hsa-mir-4640 |
Genomic Coordinates | chr6: 30890883 - 30890972 |
Description | Homo sapiens miR-4640 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4640-5p | ||||||||||||||||||||||||
Sequence | 9| UGGGCCAGGGAGCAGCUGGUGGG |31 | ||||||||||||||||||||||||
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 |
Biomarker Information |
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Gene Information | |||||||||||||||||||||
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Gene Symbol | SLIT1 | ||||||||||||||||||||
Synonyms | MEGF4, SLIL1, SLIT-1, SLIT3 | ||||||||||||||||||||
Description | slit guidance ligand 1 | ||||||||||||||||||||
Transcript | NM_003061 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SLIT1 | |||||||||||||||||||||
3'UTR of SLIT1 (miRNA target sites are highlighted) |
>SLIT1|NM_003061|3'UTR 1 CGCTGGGCGTGGACAGGCCGGTGAGGGCGGGCAAGGGGCCCCAGCCGCTGCAGCAGCGGAGACAGTCGCCAGCAGCTGGG 81 CTGGGGTGCAGGTCATCACAGGACGGCTCCTGGGCAGCTGGGCCCTCCTGGGTGGGGTGGTGCCAGAGCAGCCTTTTAAA 161 AGCAAATTGCGCCATAGCTGGGGGCAGCGGGGGTGGGCGAGGCCTGAGCTGCGGGCTGCCCTCTCCGGAAGTGCCTTGCA 241 CAAATAGGCGCTTAATAAATATTTGTTGAGTGAATGTGTGCGTGAGGTCAGGCCAAGAAGTGCAGAACGATGACACCCCT 321 CCTTACCTGCTATCTGAATCTGGAGAAGAAAAATGACAGCCTTCCAAACCAACCCTTCCCTTTGGCCTGTGGCCCAGGCT 401 GGCTTGGAACTGGGTCTGTGGCCCCAGAAGCCTCTTACCCCTCTGCGGGCAACCATGAAGTACTGTCAGCCTCCCCGGGA 481 AGCCAGCCTGGTTCATTCTGCTGCTACAGAATCTGCTGGTGGTAGGCCAGGCTCTGGAGCGGGGGTGCCGCCTCCTGCTG 561 GCCAGGGAGGGTCGGACCCTTGCCCCCTGGGCTGACTGGCAGCTCTGCAGCCACGGCTTGGGAACGAGGCTGTGGGTGGA 641 GGTGGTTCTTAGGACCAGGCCTCTGAATCCTAAAGTTCTAGCATGACTACTGTAGCTGCGAGGGCTTATGTGGAGGAAAC 721 AGTCACAGGGGCTGCTCAGGGTGGCAGACCCCACTAAAGAGGGCAGAGGGTTCTTTGCTCTAGATAAACAAACATCATCT 801 GCCTCCAGACACTGGCCACAGTAGGAGTATTGGTCCTGGGCTTCCCCAGCCACCAGTCAGCCACAAGCTGTCGGTGACCT 881 ATTGGTAGAGGGACTGGGTGTGAGGGTCTGGGCCAGGGTGCTTGACCTGGGAGCAGCTGGTTCAGAGTCCTTCACACCGC 961 AGGCCAGTAGGGAGCAGTGGAAGGGACAGTGCTCCAGGCATTGGGAAGTCCCTGCTGGCTCTATCACTCGGGGCAAACTT 1041 CTCCCCACCTGGGCCTTGGGTTCTTCAGCTATAAAATGGCCAGAGGTGGGGGGCGGGATGACTAAAGGAACAGTGCAGAC 1121 TCCCCCACTGTGGTCTTGGGAGGCCAGAGGAGTTAGAAGACCTATCTATCTATCTATCTATCTACATTGATCACATCAAA 1201 AGTATTTATGTGCCTAACCCGGGGCTGGGGATTGTGGACGTTCTGGCCTAATGGACAGATGTGAACTCATCCCAGAGCAT 1281 CGCAGGAATGACCAGGATGCCCGGGAAGAGTTGAGCTGAGTGGGGGCTCCAGCCACAGACAGCGGCCCAGGCCAGGGAGT 1361 TGCTGGCAACGAAGGAGCCAGTGGTGGAAGAAGAAGAGGCCCTGAATATACGATTGCCTGCCCACGTTGTCTTCTCTTCC 1441 ATACACAGTGAAAATGTAGAAAGATGGTTTGTGAGGCCAAACTGTGAATGGGCTAAAGGGAGGCAAAGTTGCACTCTCCT 1521 TCCCCAGAGGGCTCACCAAGAGGGCACACCCCCGGGGGTTCTGGTGGGCAACGGGGGTGAGCATGTCCCTGCCCTGGCTC 1601 CCTCCATCTGTGACCAGGAGGCATGGCTGGGTGTATGTTCAGGTGAGGCTCAGAGTGGCATTGTGTCCCTGTCCCCTGCC 1681 CAGGGCAGTGAGGGGAGCCCTTGATGCTGATTAGAAGGCTAGAACTGGGGTAGAGGTGCCTGGCATGTCTCATGCCATGG 1761 GGACTCAATCTAGCAACTGTGAGTCCTGGGGTCCCTGTGATGGGAAGAGGGCAGTGCCCTGCCCAATGTGGCAGGTGTCC 1841 TCATGGCAGGATCTGCCCCTCACCAGGGGGCTGGGATCTACTTGCTTGGAGCTCTGAGCAAGGCCACAATGCCCGCCCCC 1921 ACCCCCAAGTAGACTGCAGCCTGGGCCTCATGGGGCTTCTCCCAGGCCCACATGGCATCCCTCTCTGAGTTTCCAGGCCA 2001 CCGTGGGACCCTGCAGAGCATCTGCACCGGGCTGGATAGGGCAGAAAAGCTCAAGGGCAGCTAGCTTGCCTCTTCCCTGG 2081 AAGAAAGGTGCTCTGGGACTCACCAACCCTGAGAAAGATAGCTTTCCTGGCCACCACCATTCCCCACCACCCTGGAGAAG 2161 CCAATTCCCAGGCTTGAAGGGCACTGGCTGGCAGGAGGCCTCTTCATTCTGCAGGAGGTGGAAAGGACACCTGTAGACAG 2241 GTGATGCTCACCCCTCACCTGGCGCCATGGGGCTGGGAGGTGAGCGGCTGGCATGTTTGTTCCTAGGGAGCACCATGTGA 2321 GCTTAAGGCTCCCCTGACCGGCCCCACCACATGGCCCAGCCTCCTAGCACAGCAGCGCTGACCTCAGTGCAGTCTGAGGA 2401 TTGGAATCCACCATGAGATGATGTGAGAGCTGTGTGCCCCAGGATCAACTTTTTCTCCAACTTGGCCATCAGCCAGCGAG 2481 TTGCTAAGGACCTGAGTCAGCACTCACGTTGCCTATTCACACTCCGCTTGAAAGTCCGGAAGGTGGCTACTGCAAAATCA 2561 CCCCTCTGAGAAGTCCTCTCTCCACATCTTGTCCCCCTTTGTGAAGACCCCTAGTTCGCTCTGCATTTTAGGCATGAAGA 2641 GATACAGCAGGGTGCGTCCGGAGGGAGCTGTGGCCTTGCAACACCACTGGCAACAGGGCCGGGGCTCCCGGTGAAGGTGT 2721 CAGGAAGTGGAAAAGGCTGGACTTTGTCTCCTCTTTGCCTGCTGGTAGCCTAACCGCAAAAGTATCTCTTTATACAGAAT 2801 ACTTACAGATTCTAATATATATTTGTATTTCATTTTGTTACAGTATTTTTATATGTTAAAGTCAACATCCAGCGTCTTGT 2881 TTTGCCTTTCAGATGCTATGTGGTCGTGGCACGTTTTGTTGGGGGTTTCTGTAGTCGTCTTGTTTGGATCAACTCCTAGA 2961 GGCTGGTTTAGAACAGGCCCATGAGGGAGCTGCACCTGCCCTGGAAGTATTGTTTTAGACTATGTCGATATTGTCTGTTG 3041 TCTTCCATGTGAACATGACATTGAGTCACTCTGCAAAAAAAAAAAAAAAAAA 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 | 6585.0 | ||||||
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 GSM1065668. 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 GSM1065668 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_7 |
Location of target site | ENST00000266058.4 | 3UTR | ACAUGGCCCAGCCUCCUA |
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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87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT100106 | ABT1 | activator of basal transcription 1 | ![]() |
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2 | 8 | ||||||
MIRT248144 | LMBR1L | limb development membrane protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT327062 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 2 | ||||||
MIRT347231 | GATAD2A | GATA zinc finger domain containing 2A | ![]() |
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2 | 2 | ||||||
MIRT450221 | CENPN | centromere protein N | ![]() |
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2 | 2 | ||||||
MIRT451264 | NDUFA11 | NADH:ubiquinone oxidoreductase subunit A11 | ![]() |
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2 | 2 | ||||||
MIRT452701 | C1orf226 | chromosome 1 open reading frame 226 | ![]() |
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2 | 2 | ||||||
MIRT453212 | CERS1 | ceramide synthase 1 | ![]() |
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2 | 2 | ||||||
MIRT454822 | POLR2J3 | RNA polymerase II subunit J3 | ![]() |
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2 | 2 | ||||||
MIRT454883 | RAD50 | RAD50 double strand break repair protein | ![]() |
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2 | 2 | ||||||
MIRT455783 | TAF8 | TATA-box binding protein associated factor 8 | ![]() |
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2 | 2 | ||||||
MIRT455858 | TMEM254 | transmembrane protein 254 | ![]() |
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2 | 2 | ||||||
MIRT457615 | UPK3BL | uroplakin 3B like 1 | ![]() |
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2 | 2 | ||||||
MIRT457822 | ITPRIP | inositol 1,4,5-trisphosphate receptor interacting protein | ![]() |
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2 | 4 | ||||||
MIRT458344 | NOC2L | NOC2 like nucleolar associated transcriptional repressor | ![]() |
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2 | 2 | ||||||
MIRT458376 | ITM2C | integral membrane protein 2C | ![]() |
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2 | 2 | ||||||
MIRT458928 | SAMD4B | sterile alpha motif domain containing 4B | ![]() |
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2 | 2 | ||||||
MIRT459066 | WFIKKN2 | WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT460138 | ASB16 | ankyrin repeat and SOCS box containing 16 | ![]() |
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2 | 2 | ||||||
MIRT460818 | FSTL4 | follistatin like 4 | ![]() |
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2 | 2 | ||||||
MIRT461285 | COX10 | COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor | ![]() |
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2 | 2 | ||||||
MIRT462738 | EFNB1 | ephrin B1 | ![]() |
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2 | 2 | ||||||
MIRT464556 | UBTF | upstream binding transcription factor, RNA polymerase I | ![]() |
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2 | 2 | ||||||
MIRT477910 | DUSP2 | dual specificity phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT479073 | CNNM4 | cyclin and CBS domain divalent metal cation transport mediator 4 | ![]() |
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2 | 4 | ||||||
MIRT479534 | CDC5L | cell division cycle 5 like | ![]() |
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2 | 4 | ||||||
MIRT485628 | EEPD1 | endonuclease/exonuclease/phosphatase family domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT489896 | PPIC | peptidylprolyl isomerase C | ![]() |
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2 | 4 | ||||||
MIRT490737 | SRCIN1 | SRC kinase signaling inhibitor 1 | ![]() |
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2 | 2 | ||||||
MIRT491201 | MLLT1 | MLLT1, super elongation complex subunit | ![]() |
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2 | 4 | ||||||
MIRT492681 | PHYHIP | phytanoyl-CoA 2-hydroxylase interacting protein | ![]() |
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2 | 2 | ||||||
MIRT494593 | ATG7 | autophagy related 7 | ![]() |
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2 | 2 | ||||||
MIRT495061 | PADI3 | peptidyl arginine deiminase 3 | ![]() |
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2 | 4 | ||||||
MIRT496623 | TMEM67 | transmembrane protein 67 | ![]() |
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2 | 2 | ||||||
MIRT497177 | ZBTB40 | zinc finger and BTB domain containing 40 | ![]() |
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2 | 2 | ||||||
MIRT498217 | TLN2 | talin 2 | ![]() |
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2 | 2 | ||||||
MIRT498306 | BCL11B | B-cell CLL/lymphoma 11B | ![]() |
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2 | 2 | ||||||
MIRT499668 | NPHP3 | nephrocystin 3 | ![]() |
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2 | 2 | ||||||
MIRT508080 | ANKRD52 | ankyrin repeat domain 52 | ![]() |
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2 | 2 | ||||||
MIRT509707 | ANKRD23 | ankyrin repeat domain 23 | ![]() |
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2 | 2 | ||||||
MIRT509841 | FOS | Fos proto-oncogene, AP-1 transcription factor subunit | ![]() |
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2 | 2 | ||||||
MIRT512814 | ARRDC2 | arrestin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT513353 | SLIT1 | slit guidance ligand 1 | ![]() |
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2 | 2 | ||||||
MIRT514293 | FXYD5 | FXYD domain containing ion transport regulator 5 | ![]() |
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2 | 2 | ||||||
MIRT516598 | FAM89A | family with sequence similarity 89 member A | ![]() |
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2 | 4 | ||||||
MIRT516616 | DARS2 | aspartyl-tRNA synthetase 2, mitochondrial | ![]() |
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2 | 2 | ||||||
MIRT518348 | CCL5 | C-C motif chemokine ligand 5 | ![]() |
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2 | 2 | ||||||
MIRT520130 | WSB1 | WD repeat and SOCS box containing 1 | ![]() |
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2 | 2 | ||||||
MIRT522072 | ORAI2 | ORAI calcium release-activated calcium modulator 2 | ![]() |
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2 | 2 | ||||||
MIRT526461 | OSBPL5 | oxysterol binding protein like 5 | ![]() |
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2 | 2 | ||||||
MIRT528278 | MBL2 | mannose binding lectin 2 | ![]() |
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2 | 2 | ||||||
MIRT534844 | RAB15 | RAB15, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT542245 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT543299 | ZNF585B | zinc finger protein 585B | ![]() |
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2 | 2 | ||||||
MIRT552456 | ZNF410 | zinc finger protein 410 | ![]() |
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2 | 2 | ||||||
MIRT553641 | TJAP1 | tight junction associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT557103 | HOXA3 | homeobox A3 | ![]() |
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2 | 2 | ||||||
MIRT570782 | FANCA | Fanconi anemia complementation group A | ![]() |
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2 | 2 | ||||||
MIRT630912 | ZMAT2 | zinc finger matrin-type 2 | ![]() |
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2 | 2 | ||||||
MIRT631034 | ZNF878 | zinc finger protein 878 | ![]() |
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2 | 2 | ||||||
MIRT639017 | AAK1 | AP2 associated kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT648596 | ZYG11B | zyg-11 family member B, cell cycle regulator | ![]() |
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2 | 2 | ||||||
MIRT648939 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | ![]() |
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2 | 2 | ||||||
MIRT652834 | TACO1 | translational activator of cytochrome c oxidase I | ![]() |
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2 | 2 | ||||||
MIRT659347 | CSRP1 | cysteine and glycine rich protein 1 | ![]() |
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2 | 2 | ||||||
MIRT664163 | APOBEC3F | apolipoprotein B mRNA editing enzyme catalytic subunit 3F | ![]() |
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2 | 2 | ||||||
MIRT670511 | ZSCAN22 | zinc finger and SCAN domain containing 22 | ![]() |
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2 | 2 | ||||||
MIRT671246 | TMEM41B | transmembrane protein 41B | ![]() |
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2 | 2 | ||||||
MIRT672120 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT672313 | CD3D | CD3d molecule | ![]() |
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2 | 2 | ||||||
MIRT672543 | BRMS1L | breast cancer metastasis-suppressor 1 like | ![]() |
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2 | 2 | ||||||
MIRT673036 | SGPL1 | sphingosine-1-phosphate lyase 1 | ![]() |
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2 | 2 | ||||||
MIRT673814 | DARS | aspartyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT674858 | GINM1 | glycoprotein integral membrane 1 | ![]() |
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2 | 2 | ||||||
MIRT674970 | SH3BP2 | SH3 domain binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT675185 | KIF1C | kinesin family member 1C | ![]() |
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2 | 2 | ||||||
MIRT675219 | UGDH | UDP-glucose 6-dehydrogenase | ![]() |
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2 | 2 | ||||||
MIRT675558 | MED16 | mediator complex subunit 16 | ![]() |
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2 | 2 | ||||||
MIRT682566 | EIF4EBP1 | eukaryotic translation initiation factor 4E binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT684640 | PDE4C | phosphodiesterase 4C | ![]() |
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2 | 2 | ||||||
MIRT689722 | ATXN2 | ataxin 2 | ![]() |
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2 | 2 | ||||||
MIRT693594 | SLC39A1 | solute carrier family 39 member 1 | ![]() |
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2 | 2 | ||||||
MIRT704745 | CDKN2B | cyclin dependent kinase inhibitor 2B | ![]() |
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2 | 2 | ||||||
MIRT712779 | ZNF154 | zinc finger protein 154 | ![]() |
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2 | 2 | ||||||
MIRT718118 | OTOF | otoferlin | ![]() |
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2 | 2 | ||||||
MIRT720115 | SAMD4A | sterile alpha motif domain containing 4A | ![]() |
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2 | 2 | ||||||
MIRT720275 | EIF1AD | eukaryotic translation initiation factor 1A domain containing | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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