pre-miRNA Information
pre-miRNA hsa-mir-4708   
Genomic Coordinates chr14: 65335117 - 65335183
Description Homo sapiens miR-4708 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4708-5p
Sequence 9| AGAGAUGCCGCCUUGCUCCUU |29
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1017378847 9 dbSNP
rs750825813 10 dbSNP
rs1297395738 19 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CERS4   
Synonyms LASS4, Trh1
Description ceramide synthase 4
Transcript NM_024552   
Expression
Putative miRNA Targets on CERS4
3'UTR of CERS4
(miRNA target sites are highlighted)
>CERS4|NM_024552|3'UTR
   1 CCGGGCGGGGCTGGCTGTAAGGGGTTGCCCCCCCGCCAGTGCCTTGGATATTTCTGGGGTGACTGGACTGGCGCCCCTGG
  81 GCCACCTTTCTGGAGACAGGGAGGGCCCCACCCGGGGTGGGTGGGAAGGCTGATGATCTGTCTCCAGCCCCTTCCTTCTG
 161 CCCACCCACCCTTCTTCCCTCTGGGCAACTGGACAGATCTGGGAGCCAGCAGCTGGATGCTGTGGCTGGCCAGAGACACC
 241 TCCAGGCTGTGGCCTGGGGGCTGGGGGGAGCCCCAGGCTGAAAAGGGTCCAATTAAAACAAATGGAGCCAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' uuCCUCGUUCCGCCGUAGAga 5'
            |||||    | ||| ||  
Target 5' tgGGAGC----CAGCAGCTgg 3'
200 - 216 101.00 -10.54
2
miRNA  3' uuccucguuccgCCGUAGAga 5'
                      |||| ||  
Target 5' ttcttccctctgGGCAACTgg 3'
172 - 192 93.00 -6.54
3
miRNA  3' uuccucguuccgccGUAGAGa 5'
                        :||:|| 
Target 5' gccagtgccttggaTATTTCt 3'
35 - 55 88.00 -7.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN20079277 28 COSMIC
COSN508985 35 COSMIC
COSN24387468 74 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1045702346 1 dbSNP
rs1380012511 2 dbSNP
rs756000347 3 dbSNP
rs778998101 4 dbSNP
rs745991264 5 dbSNP
rs1044547 7 dbSNP
rs775840159 8 dbSNP
rs1466206463 9 dbSNP
rs747191982 11 dbSNP
rs1392716230 12 dbSNP
rs1204365221 14 dbSNP
rs892884825 18 dbSNP
rs776804362 19 dbSNP
rs927801585 21 dbSNP
rs1403375364 24 dbSNP
rs1234711988 25 dbSNP
rs377703774 28 dbSNP
rs772861121 28 dbSNP
rs878862385 28 dbSNP
rs1010342388 30 dbSNP
rs549602365 31 dbSNP
rs1208607853 32 dbSNP
rs765797102 34 dbSNP
rs76848957 35 dbSNP
rs751288236 36 dbSNP
rs1384350040 44 dbSNP
rs754518107 52 dbSNP
rs1028875461 57 dbSNP
rs1451209436 58 dbSNP
rs1010677887 61 dbSNP
rs189950277 63 dbSNP
rs1445063624 71 dbSNP
rs1365902867 72 dbSNP
rs549035616 73 dbSNP
rs984612646 74 dbSNP
rs1490254252 76 dbSNP
rs1016393837 83 dbSNP
rs1289637780 84 dbSNP
rs979017101 89 dbSNP
rs1029129465 93 dbSNP
rs962133111 98 dbSNP
rs953714821 102 dbSNP
rs1225960016 103 dbSNP
rs1292582256 106 dbSNP
rs1336044474 111 dbSNP
rs972501046 113 dbSNP
rs917944630 114 dbSNP
rs568738363 115 dbSNP
rs534516376 116 dbSNP
rs949376375 119 dbSNP
rs1431078805 123 dbSNP
rs1361460525 125 dbSNP
rs1167189131 140 dbSNP
rs981000358 143 dbSNP
rs547962253 145 dbSNP
rs59164681 147 dbSNP
rs1487377793 150 dbSNP
rs972346714 151 dbSNP
rs1267016882 152 dbSNP
rs530818346 153 dbSNP
rs113714656 162 dbSNP
rs371603349 163 dbSNP
rs1194522941 164 dbSNP
rs1347774461 166 dbSNP
rs1418725207 168 dbSNP
rs36260 169 dbSNP
rs945829522 171 dbSNP
rs1344076184 177 dbSNP
rs535692081 183 dbSNP
rs1411285719 187 dbSNP
rs937204042 189 dbSNP
rs1327630259 191 dbSNP
rs1408103217 192 dbSNP
rs1057200754 200 dbSNP
rs12891 204 dbSNP
rs61213498 213 dbSNP
rs1010338206 217 dbSNP
rs997556157 219 dbSNP
rs1020262560 220 dbSNP
rs1470641669 230 dbSNP
rs1463841421 236 dbSNP
rs1299116770 237 dbSNP
rs1264278503 239 dbSNP
rs904529649 243 dbSNP
rs1321847362 245 dbSNP
rs386806571 249 dbSNP
rs570160350 250 dbSNP
rs1225066083 251 dbSNP
rs36261 252 dbSNP
rs1006080344 255 dbSNP
rs1278632578 260 dbSNP
rs555356188 261 dbSNP
rs953560948 268 dbSNP
rs988067892 269 dbSNP
rs1403552227 278 dbSNP
rs1161127969 281 dbSNP
rs767377807 287 dbSNP
rs1016090124 288 dbSNP
rs750408023 293 dbSNP
rs1311900366 303 dbSNP
rs1319865760 310 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uucCUCGUUCCGCCGuagaga 5'
             |:| ::|| |||      
Target 5' aaaGGGGGGGGGGGC------ 3'
17 - 31
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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Cardiac Tissues
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 GSM2202476. RNA binding protein: AGO2. Condition:S1_LV_54yo_Male_AGO2_bound_RNA ...

- Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research.

Article - Spengler RM; Zhang X; Cheng C; McLendon JM; et al.
- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
CLIP-seq Support 1 for dataset GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000559336.1 | 3UTR | AAAAAAAAAAAAAAAAAAGGGGGGGGGGGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000559336.1 | 3UTR | CAAAAAAAAAAAAAAAAAAGGGGGGGGGGGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
94 hsa-miR-4708-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT095681 RBM27 RNA binding motif protein 27 2 4
MIRT104033 USP42 ubiquitin specific peptidase 42 2 6
MIRT114773 CMPK1 cytidine/uridine monophosphate kinase 1 2 2
MIRT246923 CCND1 cyclin D1 2 2
MIRT392569 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT443949 LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 2 2
MIRT446695 PAPPA pappalysin 1 2 2
MIRT447383 VOPP1 vesicular, overexpressed in cancer, prosurvival protein 1 2 2
MIRT449321 FAM120AOS family with sequence similarity 120A opposite strand 2 2
MIRT449717 C1orf61 chromosome 1 open reading frame 61 2 2
MIRT449738 TAB2 TGF-beta activated kinase 1/MAP3K7 binding protein 2 2 2
MIRT450531 PGLS 6-phosphogluconolactonase 2 2
MIRT455650 YARS tyrosyl-tRNA synthetase 2 2
MIRT458036 MRPL12 mitochondrial ribosomal protein L12 2 2
MIRT463468 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT466677 TAF1D TATA-box binding protein associated factor, RNA polymerase I subunit D 2 4
MIRT467789 SLC2A14 solute carrier family 2 member 14 2 2
MIRT468167 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT468652 SECISBP2L SECIS binding protein 2 like 2 6
MIRT469380 RER1 retention in endoplasmic reticulum sorting receptor 1 2 2
MIRT470346 PPP2R5E protein phosphatase 2 regulatory subunit B'epsilon 2 2
MIRT472418 NCKAP1 NCK associated protein 1 2 2
MIRT474612 KLF3 Kruppel like factor 3 2 2
MIRT478703 CSRNP2 cysteine and serine rich nuclear protein 2 2 2
MIRT481008 BBC3 BCL2 binding component 3 2 4
MIRT483098 TFPI tissue factor pathway inhibitor 2 2
MIRT485113 SHISA6 shisa family member 6 2 2
MIRT497533 ZNF607 zinc finger protein 607 2 2
MIRT500644 TUBB2A tubulin beta 2A class IIa 2 6
MIRT500890 STRN striatin 2 4
MIRT501900 MED13 mediator complex subunit 13 2 2
MIRT506646 MAPK1 mitogen-activated protein kinase 1 2 4
MIRT512675 ENO4 enolase family member 4 2 2
MIRT516977 OR7D2 olfactory receptor family 7 subfamily D member 2 2 2
MIRT528754 RPS27 ribosomal protein S27 2 6
MIRT539670 ZBTB44 zinc finger and BTB domain containing 44 2 2
MIRT544129 PPIL1 peptidylprolyl isomerase like 1 2 2
MIRT546382 STOX2 storkhead box 2 2 4
MIRT562143 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT568713 TMEM30B transmembrane protein 30B 2 2
MIRT571029 CENPP centromere protein P 2 2
MIRT572781 ZNF277 zinc finger protein 277 2 2
MIRT573162 SLC30A9 solute carrier family 30 member 9 2 2
MIRT609126 NUDT3 nudix hydrolase 3 2 2
MIRT609284 OAS3 2'-5'-oligoadenylate synthetase 3 2 2
MIRT613430 GALNT6 polypeptide N-acetylgalactosaminyltransferase 6 2 2
MIRT613770 TTC38 tetratricopeptide repeat domain 38 2 2
MIRT616645 LRAT lecithin retinol acyltransferase 2 4
MIRT630892 SLC25A33 solute carrier family 25 member 33 2 2
MIRT636526 FAXC failed axon connections homolog 2 4
MIRT641394 NUBPL nucleotide binding protein like 2 2
MIRT641412 SCN2B sodium voltage-gated channel beta subunit 2 2 2
MIRT642528 CERS4 ceramide synthase 4 2 2
MIRT643186 HYPK huntingtin interacting protein K 2 2
MIRT647800 FRMD8 FERM domain containing 8 2 2
MIRT652150 TRIM71 tripartite motif containing 71 2 2
MIRT652602 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT661606 C2orf15 chromosome 2 open reading frame 15 2 2
MIRT666339 SKAP2 src kinase associated phosphoprotein 2 2 2
MIRT670414 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT671122 ZNF573 zinc finger protein 573 2 2
MIRT671155 ANKRD9 ankyrin repeat domain 9 2 2
MIRT671338 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT671869 ZNF429 zinc finger protein 429 2 2
MIRT671974 IKZF3 IKAROS family zinc finger 3 2 2
MIRT672064 KIAA0930 KIAA0930 2 2
MIRT672654 SLC25A16 solute carrier family 25 member 16 2 4
MIRT672673 GTF2H5 general transcription factor IIH subunit 5 2 2
MIRT672771 UBE2V2 ubiquitin conjugating enzyme E2 V2 2 2
MIRT672929 LRRC2 leucine rich repeat containing 2 2 2
MIRT673159 C1orf50 chromosome 1 open reading frame 50 2 2
MIRT673272 RUNDC1 RUN domain containing 1 2 2
MIRT673332 THAP1 THAP domain containing 1 2 2
MIRT673351 SLC35F6 solute carrier family 35 member F6 2 2
MIRT673667 ZNF440 zinc finger protein 440 2 2
MIRT673904 DCTN6 dynactin subunit 6 2 2
MIRT674096 PLEKHA1 pleckstrin homology domain containing A1 2 2
MIRT674401 MYCBP MYC binding protein 2 2
MIRT674525 PRR23A proline rich 23A 2 2
MIRT674793 NPR1 natriuretic peptide receptor 1 2 2
MIRT674833 ADAMTS4 ADAM metallopeptidase with thrombospondin type 1 motif 4 2 2
MIRT675066 FGD6 FYVE, RhoGEF and PH domain containing 6 2 2
MIRT675080 CCR6 C-C motif chemokine receptor 6 2 2
MIRT675126 FSD2 fibronectin type III and SPRY domain containing 2 2 2
MIRT679401 IL10RB interleukin 10 receptor subunit beta 2 2
MIRT689229 RPS19 ribosomal protein S19 2 2
MIRT694008 PPIL4 peptidylprolyl isomerase like 4 2 2
MIRT699671 SFT2D2 SFT2 domain containing 2 2 2
MIRT706213 ACOT9 acyl-CoA thioesterase 9 2 2
MIRT706548 GJD2 gap junction protein delta 2 2 2
MIRT707418 RRP7A ribosomal RNA processing 7 homolog A 2 2
MIRT710648 GLUL glutamate-ammonia ligase 2 2
MIRT719393 NPCA1 Nasopharyngeal carcinoma 1 2 2
MIRT720166 PNPO pyridoxamine 5'-phosphate oxidase 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4708-5p Fulvestrant 17756771 NSC719276 approved sensitive High Breast Cancer cell line (MCF-7)
hsa-miR-4708-5p Tamoxifen 2733525 NSC180973 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-4708-5p Tripterygium wilfordii Hook F sensitive tissue
hsa-miR-4708-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-4708-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4708-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)

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