pre-miRNA Information
pre-miRNA hsa-mir-6839   
Genomic Coordinates chr7: 64679064 - 64679176
Description Homo sapiens miR-6839 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6839-3p
Sequence 92| UUGGGUUUUCUCUUCAAUCCAG |113
Evidence Experimental
Experiments Meta-analysis
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN15661209 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1426245091 3 dbSNP
rs533324498 6 dbSNP
rs1169594864 16 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol SERPING1   
Synonyms C1IN, C1INH, C1NH, HAE1, HAE2
Description serpin family G member 1
Transcript NM_000062   
Other Transcripts NM_001032295   
Expression
Putative miRNA Targets on SERPING1
3'UTR of SERPING1
(miRNA target sites are highlighted)
>SERPING1|NM_000062|3'UTR
   1 GACCTGCAGGATCAGGTTAGGGCGAGCGCTACCTCTCCAGCCTCAGCTCTCAGTTGCAGCCCTGCTGCTGCCTGCCTGGA
  81 CTTGGCCCCTGCCACCTCCTGCCTCAGGTGTCCGCTATCCACCAAAAGGGCTCCCTGAGGGTCTGGGCAAGGGACCTGCT
 161 TCTATTAGCCCTTCTCCATGGCCCTGCCATGCTCTCCAAACCACTTTTTGCAGCTTTCTCTAGTTCAAGTTCACCAGACT
 241 CTATAAATAAAACCTGACAGACCATGACTTTCAAAAAAAAAAAAAAAAAA
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' gaccuaacuUCUCUUUUGGGUu 5'
                   | | ||||||:: 
Target 5' agactctatAAATAAAACCTGa 3'
236 - 257 117.00 -5.60
2
miRNA  3' gaccuaacuucucuUUUGGguu 5'
                        |||||   
Target 5' ctgccatgctctccAAACCact 3'
184 - 205 100.00 -5.60
3
miRNA  3' gaCCUA-ACUUCUCUUUUGGGUu 5'
            ||:| ||:: | :::|||:: 
Target 5' gaGGGTCTGGGCAAGGGACCTGc 3'
137 - 159 96.00 -11.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
878165 67 ClinVar
COSN30448599 11 COSMIC
COSN19768388 21 COSMIC
COSN30119963 28 COSMIC
COSN30521980 29 COSMIC
COSN26994383 36 COSMIC
COSN23019108 46 COSMIC
COSN32050925 77 COSMIC
COSN30109131 80 COSMIC
COSN25818808 102 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1400756473 2 dbSNP
rs771960340 4 dbSNP
rs780052213 7 dbSNP
rs1012901136 8 dbSNP
rs1240934870 11 dbSNP
rs932271270 21 dbSNP
rs759505176 22 dbSNP
rs565084968 24 dbSNP
rs374568487 25 dbSNP
rs904412322 28 dbSNP
rs761601555 29 dbSNP
rs1187138261 30 dbSNP
rs1485927631 31 dbSNP
rs769568260 32 dbSNP
rs1237625875 35 dbSNP
rs774916635 36 dbSNP
rs759959495 38 dbSNP
rs1202759426 41 dbSNP
rs767708626 45 dbSNP
rs1251506361 49 dbSNP
rs1057919 50 dbSNP
rs1405104532 57 dbSNP
rs3205379 58 dbSNP
rs1415998852 59 dbSNP
rs1357912766 60 dbSNP
rs1306606413 63 dbSNP
rs998696963 65 dbSNP
rs899262177 67 dbSNP
rs1169896321 70 dbSNP
rs1390634605 71 dbSNP
rs1031469944 74 dbSNP
rs1165737831 76 dbSNP
rs190139326 79 dbSNP
rs765115304 89 dbSNP
rs1259492502 97 dbSNP
rs1179812169 103 dbSNP
rs1044921353 112 dbSNP
rs905046736 114 dbSNP
rs1340965520 118 dbSNP
rs998378583 124 dbSNP
rs1003451362 126 dbSNP
rs1337645746 130 dbSNP
rs1450065184 132 dbSNP
rs1442060193 140 dbSNP
rs1028061890 144 dbSNP
rs953870466 145 dbSNP
rs1035384915 158 dbSNP
rs1390288708 159 dbSNP
rs1165804047 169 dbSNP
rs1016933548 171 dbSNP
rs1409789888 179 dbSNP
rs963566246 182 dbSNP
rs892135095 194 dbSNP
rs1469506273 202 dbSNP
rs1009241091 203 dbSNP
rs1183715176 206 dbSNP
rs1229261732 216 dbSNP
rs1251963017 221 dbSNP
rs1270241385 227 dbSNP
rs1022020926 234 dbSNP
rs967804221 242 dbSNP
rs1223724637 246 dbSNP
rs548006931 256 dbSNP
rs1281710733 265 dbSNP
rs1231489170 266 dbSNP
rs1029144990 267 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 GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb HITS-CLIP data was present in GSM1084079. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_AbnovaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gaccuaaCUUCUCUUUUGG-GUu 5'
                 ||:| |:|:::: || 
Target 5' ---ccaaGAGGUGGAGGUUGCAg 3'
1 - 20
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]
CLIP-seq Support 1 for dataset GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000278407.4 | 3UTR | CCAAGAGGUGGAGGUUGCAGU
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 GSM1084079
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_hippuristanol_rep2_AbnovaAb
Location of target site ENST00000278407.4 | 3UTR | CCAAGAGGUGGAGGUUGCAGU
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
62 hsa-miR-6839-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059162 TXNIP thioredoxin interacting protein 2 2
MIRT064872 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT065802 HOXC8 homeobox C8 2 4
MIRT106005 SDCBP syndecan binding protein 2 2
MIRT275773 TFDP1 transcription factor Dp-1 2 2
MIRT314032 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 2
MIRT360277 HIST1H2BE histone cluster 1 H2B family member e 2 8
MIRT360301 HIST1H2BH histone cluster 1 H2B family member h 2 2
MIRT450086 OR2A4 olfactory receptor family 2 subfamily A member 4 2 2
MIRT468815 RSRC2 arginine and serine rich coiled-coil 2 2 6
MIRT475093 IRF2BP2 interferon regulatory factor 2 binding protein 2 2 4
MIRT477575 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
MIRT483926 LCORL ligand dependent nuclear receptor corepressor like 2 6
MIRT504381 HIST1H1C histone cluster 1 H1 family member c 2 4
MIRT506970 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT507028 HIST1H3B histone cluster 1 H3 family member b 2 6
MIRT511561 HIST3H2BB histone cluster 3 H2B family member b 2 4
MIRT511650 HIST1H3D histone cluster 1 H3 family member d 2 6
MIRT511696 HIST1H2BL histone cluster 1 H2B family member l 2 4
MIRT511737 HIST1H2BB histone cluster 1 H2B family member b 2 6
MIRT511746 HIST1H2BA histone cluster 1 H2B family member a 2 8
MIRT515260 CSNK1E casein kinase 1 epsilon 2 2
MIRT516220 RAB3B RAB3B, member RAS oncogene family 2 4
MIRT523281 HIST1H1E histone cluster 1 H1 family member e 2 2
MIRT524121 DMXL1 Dmx like 1 2 2
MIRT530744 GPR82 G protein-coupled receptor 82 2 2
MIRT532214 CCDC117 coiled-coil domain containing 117 2 2
MIRT546182 TPRG1L tumor protein p63 regulated 1 like 2 2
MIRT558638 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT559562 ARF1 ADP ribosylation factor 1 2 4
MIRT560680 HIST1H1T histone cluster 1 H1 family member t 2 2
MIRT570746 AAK1 AP2 associated kinase 1 2 2
MIRT609518 RAB3IP RAB3A interacting protein 2 2
MIRT612583 SYNGAP1 synaptic Ras GTPase activating protein 1 2 4
MIRT615733 RIOK3 RIO kinase 3 2 2
MIRT616068 SIX1 SIX homeobox 1 2 2
MIRT617903 SGCD sarcoglycan delta 2 2
MIRT620851 SERPING1 serpin family G member 1 2 2
MIRT625107 SLC1A5 solute carrier family 1 member 5 2 2
MIRT625120 NUP93 nucleoporin 93 2 2
MIRT625893 LINC00632 long intergenic non-protein coding RNA 632 2 2
MIRT626569 MED7 mediator complex subunit 7 2 2
MIRT626694 ZFP14 ZFP14 zinc finger protein 2 4
MIRT626808 PRR11 proline rich 11 2 2
MIRT628131 HM13 histocompatibility minor 13 2 2
MIRT636596 DCAF5 DDB1 and CUL4 associated factor 5 2 2
MIRT649866 SLFN12L schlafen family member 12 like 2 2
MIRT652133 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652663 TIMELESS timeless circadian clock 2 2
MIRT658335 FAM83D family with sequence similarity 83 member D 2 2
MIRT660615 ANKS4B ankyrin repeat and sterile alpha motif domain containing 4B 2 2
MIRT666304 SLC22A3 solute carrier family 22 member 3 2 2
MIRT668528 ERGIC2 ERGIC and golgi 2 2 2
MIRT692510 PARD3 par-3 family cell polarity regulator 2 2
MIRT694784 DHFRL1 dihydrofolate reductase 2 2 2
MIRT700510 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT701438 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT710155 MTRF1L mitochondrial translational release factor 1 like 2 2
MIRT711436 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT716979 GPR155 G protein-coupled receptor 155 2 2
MIRT720155 POU2F2 POU class 2 homeobox 2 2 2
MIRT722512 DSTYK dual serine/threonine and tyrosine protein kinase 2 2

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