pre-miRNA Information | |
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pre-miRNA | hsa-mir-3622a |
Genomic Coordinates | chr8: 27701677 - 27701759 |
Description | Homo sapiens miR-3622a stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3622a-5p | |||||||||||||||||||||||||||||||||||
Sequence | 14| CAGGCACGGGAGCUCAGGUGAG |35 | |||||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | APAF1 | ||||||||||||||||||||
Synonyms | APAF-1, CED4 | ||||||||||||||||||||
Description | apoptotic peptidase activating factor 1 | ||||||||||||||||||||
Transcript | NM_181869 | ||||||||||||||||||||
Other Transcripts | NM_013229 , NM_181861 , NM_181868 , NM_001160 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on APAF1 | |||||||||||||||||||||
3'UTR of APAF1 (miRNA target sites are highlighted) |
>APAF1|NM_181869|3'UTR 1 GAAAATACACGTGTCCCCTGACTTCAAAACATATGTGACTGTGGATAATCTTGGTATTTTATATATTTTACAGACTTTAG 81 AATAAAATAGTTAAGCATTAATGTAGTTGAACTTTTTAAATTTTTGAATTGGAAAAAAATTCTAATGAAACCCTGATATC 161 AACTTTTTATAAAGCTCTTAATTGTTGTGCAGTATTGCATTCATTACAAAAGTGTTTGTGGTTGGATGAATAATATTAAT 241 GTAGCTTTTTCCCAAATGAACATACCTTTAATCTTGTTTTTCATGATCATCATTAACAGTTTGTCCTTAGGATGCAAATG 321 AAAATGTGAATACATACCTTGTTGTACTGTTGGTAAAATTCTGTCTTGATGCATTCAAAATGGTTGACATAATTAATGAG 401 AAGAATTTGGAAGAAATTGGTATTTTAATACTGTCTGTATTTATTACTGTTATGCAGGCTGTGCCTCAGGGTAGCAGTGG 481 CCTGCTTTTTGAACCACACTTACCCCAAGGGGGTTTTGTTCTCCTAAATACAATCTTAGAGGTTTTTTGCACTCTTTAAA 561 TTTGCTTTAAAAATATTGTGTCTGTGTGCATAGTCTGCAGCATTTCCTTTAATTGACTCAATAAGTGAGTCTTGGATTTA 641 GCAGGCCCCCCCACCTTTTTTTTTTGTTTTTGGAGACAGAGTCTTGCTTTGTTGCCAGGCTGGAGTGCAGTGGCGCGATC 721 TCGGCTCACCACAATCGCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGT 801 GCGCACATGCCAGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCGGGATGGTCTCGATCTCTTG 881 ACCTCATGATCTACCCGCCTTGGCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCCACCGTGCCTGGCCAGGCCCCTTCT 961 CTTTTAATGGAGACAGGGTCTTGCACTATCACCCAGGCTGGAGTGCAGTGGCATAATCATACCTCATTGCAGCCTCAGAC 1041 TCCTGGGTTCAAGCAATCCTCCTGCCTCAGCCTCCCAAGTAGCTGAGACTACAGGCACGAGCCACCACACCCAGCTAATT 1121 TTTAAGTTTTCTTGTAGAGACAGGGTCTCACTATGTTGTCTAGGCTGGTCTTGAACTCTTGGCCTCAAGTAATCCTCCTG 1201 CCTCAGCCTCCCAAAGTGTTGGGATTGCAGATATGAGCCACTGGCCTGGCCTTCAGCAGTTCTTTTTGTGAAGTAAAACT 1281 TGTATGTTGGAAAGAGTAGATTTTATTGGTCTACCCTTTTCTCACTGTAGCTGCTGGCAGCCCTGTGCCATATCTGGACT 1361 CTAGTTGTCAGTATCTGAGTTGGACACTATTCCTGCTCCCTCTTGTTTCTTACATATCAGACTTCTTACTTGAATGAAAC 1441 CTGATCTTTCCTAATCCTCACTTTTTTCTTTTTTAAAAAGCAGTTTCTCCACTGCTAAATGTTAGTCATTGAGGTGGGGC 1521 CAATTTTAATCATAAGCCTTAATAAGATTTTTCTAAGAAATGTGAAATAGAACAATTTTCATCTAATTCCATTTACTTTT 1601 AGATGAATGGCATTGTGAATGCCATTCTTTTAATGAATTTCAAGAGAATTCTCTGGTTTTCTGTGTAATTCCAGATGAGT 1681 CACTGTAACTCTAGAAGATTAACCTTCCAGCCAACCTATTTTCCTTTCCCTTGTCTCTCTCATCCTCTTTTCCTTCCTTC 1761 TTTCCTTTCTCTTCTTTTATCTCCAAGGTTAATCAGGAAAAATAGCTTTTGACAGGGGAAAAAACTCAATAACTAGCTAT 1841 TTTTGACCTCCTGATCAGGAACTTTAGTTGAAGCGTAAATCTAAAGAAACATTTTCTCTGAAATATATTATTAAGGGCAA 1921 TGGAGATAAATTAATAGTAGATGTGGTTCCCAGAAAATATAATCAAAATTCAAAGATTTTTTTTGTTTCTGTAACTGGAA 2001 CTAAATCAAATGATTACTAGTGTTAATAGTAGATAACTTGTTTTTATTGTTGGTGCATATTAGTATAACTGTGGGGTAGG 2081 TCGGGGAGAGGGTAAGGGAATAGATCACTCAGATGTATTTTAGATAAGCTATTTAGCCTTTGATGGAATCATAAATACAG 2161 TGAATACAATCCTTTGCATTGTTAAGGAGGTTTTTTGTTTTTAAATGGTGGGTCAAGGAGCTAGTTTACAGGCTTACTGT 2241 GATTTAAGCAAATGTGAAAAGTGAAACCTTAATTTTATCAAAAGAAATTTCTGTAAATGGTATGTCTCCTTAGAATACCC 2321 AAATCATAATTTTATTTGTACACACTGTTAGGGGCTCATCTCATGTAGGCAGAGTATAAAGTATTACCTTTTGGAATTAA 2401 AAGCCACTGACTGTTATAAAGTATAACAACACACATCAGGTTTTAAAAAGCCTTGAATGGCCCTTGTCTTAAAAAGAAAT 2481 TAGGAGCCAGGTGCGGTGGCACGTGCCTGTAATCCCAGCTCCTTGGGAGGCTAAGACAGGAGGATTCCTTGAGCCCTGGA 2561 GTTTGAGTCCAGCCTGGGTGACATAGCAAGACCCTGTCTTAAAAGAAAAATGGGAAGAAAGACAAGGTAACATGAAGAAA 2641 GAAGAGATACCTAGTATGATGGAGCTGCAAATTTCATGGCAGTTCATGCAGTCGGTCAAGAGGAGGATTTTGTTTTGTAG 2721 TTTGCAGATGAGCATTTCTAAAGCATTTTCCCTTGCTGTATTTTTTTGTATTATAAATTACATTGGACTTCATATATATA 2801 ATTTTTTTTTACATTATATGTCTCTTGTATGTTTTGAAACTCTTGTATTTATGATATAGCTTATATGATTTTTTTGCCTT 2881 GGTATACATTTTAAAATATGAATTTAAAAAATTTTTGTAAAAATAAAATTCACAAAATTGTTTTGAAAAACAAAAAAAAA 2961 AAAAA 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 | HEK293S | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM1084045. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep3
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Karginov FV; Hannon GJ - Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
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CLIP-seq Support 1 for dataset GSM4903834 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_b |
Location of target site | NM_181868 | 3UTR | AAAAAGAAAUUAGGAGCCAGGUGCGGUGGCAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903835 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_181869 | 3UTR | CAUCAGGUUUUAAAAAGCCUUGAAUGGCCCUUGUCUUAAAAAGAAAUUAGGAGCCAGGUGCGGUGGCACGUGCCUGUAAUCCCAGCUCCUUGGGAGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_181868 | 3UTR | AGGUGCGGUGGCACGUGCCUGUAAUCCCAGCUCCUUGGGAGGCUAAGACAGGAGGAUUCCUUGAGCCCUGGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903837 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_181869 | 3UTR | UUGAAUGGCCCUUGUCUUAAAAAGAAAUUAGGAGCCAGGUGCGGUGGCACGUGCCUGUAAUCCCAGCUCCUUGGGAGG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM4903838 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_181861 | 3UTR | AGGUGCGGUGGCACGUGCCUGUAAUCCCAGCUCCUUGGGAGGCUAAGACAGGAGGAUUCCUUGAGCCCUGGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM1084045 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_arsenite_rep3 |
Location of target site | ENST00000333991.1 | 3UTR | UUACAGGCGUGAGCCACCGUGCCUGGCCAGGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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61 hsa-miR-3622a-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT166678 | ZSWIM6 | zinc finger SWIM-type containing 6 | ![]() |
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2 | 2 | ||||||
MIRT452081 | ATP6V0B | ATPase H+ transporting V0 subunit b | ![]() |
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2 | 2 | ||||||
MIRT457039 | S1PR3 | sphingosine-1-phosphate receptor 3 | ![]() |
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2 | 2 | ||||||
MIRT471975 | NR3C1 | nuclear receptor subfamily 3 group C member 1 | ![]() |
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2 | 2 | ||||||
MIRT474065 | LMNB2 | lamin B2 | ![]() |
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2 | 2 | ||||||
MIRT475862 | H6PD | hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase | ![]() |
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2 | 2 | ||||||
MIRT476191 | GOLGA8A | golgin A8 family member A | ![]() |
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2 | 2 | ||||||
MIRT476521 | GABRB1 | gamma-aminobutyric acid type A receptor beta1 subunit | ![]() |
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2 | 2 | ||||||
MIRT483046 | C15orf52 | chromosome 15 open reading frame 52 | ![]() |
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2 | 4 | ||||||
MIRT495541 | EIF3H | eukaryotic translation initiation factor 3 subunit H | ![]() |
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2 | 2 | ||||||
MIRT495892 | CLOCK | clock circadian regulator | ![]() |
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2 | 2 | ||||||
MIRT495992 | LTBP2 | latent transforming growth factor beta binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT496001 | EMP1 | epithelial membrane protein 1 | ![]() |
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2 | 2 | ||||||
MIRT496208 | PLEKHG2 | pleckstrin homology and RhoGEF domain containing G2 | ![]() |
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2 | 2 | ||||||
MIRT496427 | ACTRT3 | actin related protein T3 | ![]() |
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2 | 2 | ||||||
MIRT496438 | ZNF704 | zinc finger protein 704 | ![]() |
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2 | 2 | ||||||
MIRT496473 | SDE2 | SDE2 telomere maintenance homolog | ![]() |
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2 | 2 | ||||||
MIRT496555 | TBX15 | T-box 15 | ![]() |
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2 | 2 | ||||||
MIRT497202 | CECR1 | adenosine deaminase 2 | ![]() |
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2 | 2 | ||||||
MIRT507632 | CREBZF | CREB/ATF bZIP transcription factor | ![]() |
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2 | 2 | ||||||
MIRT513377 | MGAT4A | mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A | ![]() |
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2 | 2 | ||||||
MIRT523460 | GOLGA8J | golgin A8 family member J | ![]() |
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2 | 2 | ||||||
MIRT523465 | GOLGA8I | golgin A8 family member I, pseudogene | ![]() |
1 | 1 | |||||||
MIRT526049 | GMDS | GDP-mannose 4,6-dehydratase | ![]() |
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2 | 2 | ||||||
MIRT533122 | YIPF4 | Yip1 domain family member 4 | ![]() |
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2 | 2 | ||||||
MIRT534183 | SLC8A1 | solute carrier family 8 member A1 | ![]() |
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2 | 2 | ||||||
MIRT556618 | LCOR | ligand dependent nuclear receptor corepressor | ![]() |
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2 | 2 | ||||||
MIRT563361 | WHSC1 | nuclear receptor binding SET domain protein 2 | ![]() |
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2 | 2 | ||||||
MIRT563868 | FAM206A | family with sequence similarity 206 member A | ![]() |
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2 | 2 | ||||||
MIRT564360 | PPWD1 | peptidylprolyl isomerase domain and WD repeat containing 1 | ![]() |
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2 | 2 | ||||||
MIRT564661 | ZNF449 | zinc finger protein 449 | ![]() |
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2 | 2 | ||||||
MIRT564805 | ZBTB33 | zinc finger and BTB domain containing 33 | ![]() |
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2 | 2 | ||||||
MIRT564867 | ZBED3 | zinc finger BED-type containing 3 | ![]() |
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2 | 2 | ||||||
MIRT565340 | TMEM104 | transmembrane protein 104 | ![]() |
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2 | 2 | ||||||
MIRT566439 | PHF16 | jade family PHD finger 3 | ![]() |
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2 | 2 | ||||||
MIRT567587 | FCHSD2 | FCH and double SH3 domains 2 | ![]() |
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2 | 2 | ||||||
MIRT569597 | C3orf62 | chromosome 3 open reading frame 62 | ![]() |
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2 | 2 | ||||||
MIRT569700 | FMNL3 | formin like 3 | ![]() |
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2 | 2 | ||||||
MIRT575957 | Nanos1 | nanos homolog 1 (Drosophila) | ![]() |
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2 | 3 | ||||||
MIRT576516 | Slc35e2 | solute carrier family 35, member E2 | ![]() |
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2 | 2 | ||||||
MIRT608480 | RRP36 | ribosomal RNA processing 36 | ![]() |
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2 | 2 | ||||||
MIRT614335 | NANOS1 | nanos C2HC-type zinc finger 1 | ![]() |
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2 | 3 | ||||||
MIRT630816 | ATAT1 | alpha tubulin acetyltransferase 1 | ![]() |
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2 | 4 | ||||||
MIRT631708 | C1QTNF6 | C1q and TNF related 6 | ![]() |
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2 | 2 | ||||||
MIRT632369 | SRRD | SRR1 domain containing | ![]() |
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2 | 2 | ||||||
MIRT633471 | DSN1 | DSN1 homolog, MIS12 kinetochore complex component | ![]() |
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2 | 2 | ||||||
MIRT634478 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT667336 | MTHFD1L | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like | ![]() |
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2 | 2 | ||||||
MIRT667654 | LFNG | LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase | ![]() |
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2 | 2 | ||||||
MIRT671046 | SS18 | SS18, nBAF chromatin remodeling complex subunit | ![]() |
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2 | 2 | ||||||
MIRT672823 | VEZT | vezatin, adherens junctions transmembrane protein | ![]() |
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2 | 2 | ||||||
MIRT673049 | SGPL1 | sphingosine-1-phosphate lyase 1 | ![]() |
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2 | 2 | ||||||
MIRT673435 | APAF1 | apoptotic peptidase activating factor 1 | ![]() |
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2 | 2 | ||||||
MIRT676096 | DPP9 | dipeptidyl peptidase 9 | ![]() |
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2 | 2 | ||||||
MIRT678059 | RPL7L1 | ribosomal protein L7 like 1 | ![]() |
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2 | 2 | ||||||
MIRT679783 | GOLGA2 | golgin A2 | ![]() |
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2 | 2 | ||||||
MIRT684219 | C9orf64 | chromosome 9 open reading frame 64 | ![]() |
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2 | 2 | ||||||
MIRT697642 | WRN | Werner syndrome RecQ like helicase | ![]() |
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2 | 2 | ||||||
MIRT706595 | C1RL | complement C1r subcomponent like | ![]() |
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2 | 2 | ||||||
MIRT706603 | CCS | copper chaperone for superoxide dismutase | ![]() |
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2 | 2 | ||||||
MIRT717647 | HLX | H2.0 like homeobox | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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