pre-miRNA Information
pre-miRNA hsa-mir-4680   
Genomic Coordinates chr10: 110898090 - 110898155
Description Homo sapiens miR-4680 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4680-5p
Sequence 5| AGAACUCUUGCAGUCUUAGAUGU |27
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1274530692 2 dbSNP
rs780271274 5 dbSNP
rs1461423681 7 dbSNP
rs749729920 8 dbSNP
rs1252920446 10 dbSNP
rs201739274 11 dbSNP
rs774971106 19 dbSNP
rs748132091 22 dbSNP
rs773643180 22 dbSNP
rs1235425484 23 dbSNP
Putative Targets

Gene Information
Gene Symbol SEC24D   
Synonyms CLCRP2
Description SEC24 homolog D, COPII coat complex component
Transcript NM_014822   
Expression
Putative miRNA Targets on SEC24D
3'UTR of SEC24D
(miRNA target sites are highlighted)
>SEC24D|NM_014822|3'UTR
   1 TTGAAACTTCTCTGTCATTGATGTTGCATTTCCAAGGAGATAATCTCCTTCTTGGTGCCTAATTTTCTAGATGATAATAG
  81 GCTAGTTTTGATTTCTTGCTCATTTTCAGAATAACTTTCCAGGAAGAGATGGCATTTAGAACTTCAGCTTTGGTGCTCAG
 161 GTATAAAGCCAATTAAGGTACAATTGTACCATAAAGGGAACAATCTGTTTCTGATTGCACAGTTTCTAATTTTTAAAACT
 241 GATGTGGTTTGCATTTCATAAAAGGCAAAGTTTACAGAACCATAAACATTCTCAATTTTCTTTATGCTAGACATATAAAT
 321 TATTTTTCAAACTGTATAGATTTGGGGTAAAAAGTTGTCTCAGTTCCTCTCCCAATTGCAATGAGAAAAAAAAGCTTAAT
 401 TTTTACATTATACTTAATTTTCTAAAACCATGTAACTCCATTGAACACATTTTTCAACTTAAGGTCTGCATAGCAGACTT
 481 TTAATAACCTTGGGATTTATCTGGTAGAACAATATGTGTTCTACATTTTTTTCATAATTATATATTGTGTATGTTAAAAC
 561 TATTTTCCAGTTGTTTTGTCTGTAAAACTGTCTTTATCAATATGCTTAATGGTTCTTTGTACAATTTTGAAAGTTTCTAC
 641 CTGTATATAATGGATGTTAACCAGTATCAATAAATCACTTCGTATAATCTTAAAAAAAAAAAAAAA
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' ugUAGAUUCU-GACGU----UCUCAAGa 5'
            | :||||: |||||    ||| ||: 
Target 5' caACTTAAGGTCTGCATAGCAGACTTTt 3'
455 - 482 119.00 -9.80
2
miRNA  3' ugUAGAUUCUGACGUUCUCAAGa 5'
            :|:|  ||:||| | ||||: 
Target 5' ctGTTTCTGATTGC-ACAGTTTc 3'
205 - 226 116.00 -10.30
3
miRNA  3' ugUAGAUUCUGACG--UUCUCAAGa 5'
            ||| || | |||  || :|||| 
Target 5' ttATC-AATA-TGCTTAATGGTTCt 3'
594 - 616 113.00 -6.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1181948 172 ClinVar
COSN30152377 47 COSMIC
COSN5051480 71 COSMIC
COSN30150847 126 COSMIC
COSN31527335 212 COSMIC
COSN29395316 265 COSMIC
COSN31523924 397 COSMIC
COSN31609148 425 COSMIC
COSN31530561 681 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1486077264 1 dbSNP
rs1186702152 2 dbSNP
rs768293988 3 dbSNP
rs768845637 7 dbSNP
rs747558960 8 dbSNP
rs1425372432 10 dbSNP
rs1165077788 12 dbSNP
rs1193851720 18 dbSNP
rs1407857251 19 dbSNP
rs1399423418 20 dbSNP
rs775824353 25 dbSNP
rs374214917 26 dbSNP
rs1223123144 29 dbSNP
rs745928760 35 dbSNP
rs1311274871 36 dbSNP
rs779170223 37 dbSNP
rs757454816 38 dbSNP
rs749450416 39 dbSNP
rs1279082994 41 dbSNP
rs1489357830 44 dbSNP
rs760263151 45 dbSNP
rs777624625 48 dbSNP
rs755825038 50 dbSNP
rs775267354 50 dbSNP
rs1276753000 51 dbSNP
rs550715370 65 dbSNP
rs1029179283 74 dbSNP
rs1221941902 78 dbSNP
rs1165157135 84 dbSNP
rs1422346828 111 dbSNP
rs1354146658 114 dbSNP
rs187212597 116 dbSNP
rs752205242 118 dbSNP
rs1430839523 119 dbSNP
rs370583638 122 dbSNP
rs1020255967 128 dbSNP
rs1231769944 139 dbSNP
rs563055755 146 dbSNP
rs1186310846 148 dbSNP
rs1488972618 153 dbSNP
rs1010280635 156 dbSNP
rs79586191 172 dbSNP
rs1220604364 183 dbSNP
rs1409429683 184 dbSNP
rs1036041279 190 dbSNP
rs772945797 193 dbSNP
rs1377682455 198 dbSNP
rs905664609 200 dbSNP
rs1435514935 201 dbSNP
rs1328446944 204 dbSNP
rs1048234041 211 dbSNP
rs1056062720 213 dbSNP
rs931028218 215 dbSNP
rs939012823 282 dbSNP
rs1377620436 289 dbSNP
rs886227272 293 dbSNP
rs1277877387 294 dbSNP
rs1358965383 315 dbSNP
rs1271931457 323 dbSNP
rs1275489976 323 dbSNP
rs1229644498 335 dbSNP
rs1309200864 336 dbSNP
rs1239285595 337 dbSNP
rs771838798 342 dbSNP
rs1192328292 345 dbSNP
rs1047454060 357 dbSNP
rs1435729414 359 dbSNP
rs1167555613 375 dbSNP
rs1394682696 378 dbSNP
rs1801879 379 dbSNP
rs1036649593 384 dbSNP
rs930501098 391 dbSNP
rs1329671191 394 dbSNP
rs1393878288 394 dbSNP
rs943733974 408 dbSNP
rs1440017976 412 dbSNP
rs1301176672 422 dbSNP
rs1372825156 428 dbSNP
rs1213916740 430 dbSNP
rs1345976416 436 dbSNP
rs1337083998 441 dbSNP
rs1304710054 445 dbSNP
rs574247912 448 dbSNP
rs145220003 453 dbSNP
rs1212288726 463 dbSNP
rs932264782 466 dbSNP
rs1255514712 469 dbSNP
rs540231026 470 dbSNP
rs974958793 471 dbSNP
rs1476491780 476 dbSNP
rs943270588 478 dbSNP
rs1417183264 500 dbSNP
rs1459945351 504 dbSNP
rs922060918 510 dbSNP
rs978954317 514 dbSNP
rs1317322092 515 dbSNP
rs1324486850 521 dbSNP
rs1229083234 523 dbSNP
rs182872788 525 dbSNP
rs1170438416 532 dbSNP
rs1230990266 534 dbSNP
rs15128 543 dbSNP
rs987506059 545 dbSNP
rs140430151 547 dbSNP
rs1489118290 547 dbSNP
rs956025156 556 dbSNP
rs1260029155 560 dbSNP
rs1032198616 561 dbSNP
rs1481040071 562 dbSNP
rs978857583 566 dbSNP
rs1431960926 576 dbSNP
rs571060983 578 dbSNP
rs1474253791 584 dbSNP
rs1197670102 593 dbSNP
rs764781096 594 dbSNP
rs144149070 596 dbSNP
rs1458301721 596 dbSNP
rs1382424406 600 dbSNP
rs968786826 604 dbSNP
rs1023134408 609 dbSNP
rs191831989 615 dbSNP
rs1354484911 617 dbSNP
rs896103787 618 dbSNP
rs1294552965 619 dbSNP
rs988793641 619 dbSNP
rs1321818002 620 dbSNP
rs1259492836 622 dbSNP
rs146746449 624 dbSNP
rs1452152388 625 dbSNP
rs1217869026 639 dbSNP
rs1203792276 648 dbSNP
rs1257038843 653 dbSNP
rs1035708063 661 dbSNP
rs1324148094 663 dbSNP
rs1190357187 664 dbSNP
rs186928596 670 dbSNP
rs547651736 680 dbSNP
rs149722407 681 dbSNP
rs553245330 682 dbSNP
rs1362047832 687 dbSNP
rs1421269358 692 dbSNP
rs1159075265 693 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 GSM1084042. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep2 HITS-CLIP data was present in GSM1084043. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep2 ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugUAGAUUCUGACGUUCUCAAGa 5'
            | :|:||::  ||:|||||| 
Target 5' ucACUUGAGGU--CAGGAGUUCa 3'
15 - 35
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 GSM1084042
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep2
Location of target site ENST00000429811.2 | 3UTR | GCAGGUGGAUCACUUGAGGUCAGGAGUUCAAGACCA
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 GSM1084043
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep2
Location of target site ENST00000429811.2 | 3UTR | CCAAGGCAGGUGGAUCACUUGAGGUCAGGAGUUCAA
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
133 hsa-miR-4680-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT378771 MACC1 MACC1, MET transcriptional regulator 2 2
MIRT393867 ZDHHC21 zinc finger DHHC-type containing 21 2 4
MIRT446684 C2CD2 C2 calcium dependent domain containing 2 2 2
MIRT447600 MRPL3 mitochondrial ribosomal protein L3 2 2
MIRT450708 RNF152 ring finger protein 152 2 2
MIRT450784 PAPOLG poly(A) polymerase gamma 2 2
MIRT454623 COL23A1 collagen type XXIII alpha 1 chain 2 8
MIRT461620 PTCD3 pentatricopeptide repeat domain 3 2 2
MIRT462695 SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 2 2
MIRT475530 HOXA3 homeobox A3 2 8
MIRT475739 HERPUD1 homocysteine inducible ER protein with ubiquitin like domain 1 2 4
MIRT489676 CYP1A1 cytochrome P450 family 1 subfamily A member 1 2 2
MIRT490610 SLC47A1 solute carrier family 47 member 1 2 2
MIRT493628 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT496152 RPS15A ribosomal protein S15a 2 2
MIRT499232 VAV3 vav guanine nucleotide exchange factor 3 2 4
MIRT501496 PRICKLE2 prickle planar cell polarity protein 2 2 2
MIRT507163 GAS2L3 growth arrest specific 2 like 3 2 2
MIRT512389 MTRNR2L1 MT-RNR2-like 1 2 4
MIRT514626 MTRNR2L7 MT-RNR2-like 7 2 2
MIRT517474 PEX26 peroxisomal biogenesis factor 26 2 2
MIRT525332 CNGB1 cyclic nucleotide gated channel beta 1 2 2
MIRT526685 BAK1 BCL2 antagonist/killer 1 2 2
MIRT527317 CCR2 C-C motif chemokine receptor 2 2 2
MIRT527608 EYS eyes shut homolog (Drosophila) 2 2
MIRT528794 RAB32 RAB32, member RAS oncogene family 2 2
MIRT531048 TIPARP TCDD inducible poly(ADP-ribose) polymerase 2 2
MIRT532254 TBPL2 TATA-box binding protein like 2 2 2
MIRT533801 TMED7 transmembrane p24 trafficking protein 7 2 4
MIRT535887 MLEC malectin 2 2
MIRT540704 PDPK1 3-phosphoinositide dependent protein kinase 1 2 4
MIRT544645 PHF8 PHD finger protein 8 2 4
MIRT545760 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 2 2
MIRT555310 PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 2 2
MIRT555877 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 4
MIRT559507 ARID5B AT-rich interaction domain 5B 2 2
MIRT560448 SLC30A7 solute carrier family 30 member 7 2 2
MIRT561262 ZIK1 zinc finger protein interacting with K protein 1 2 2
MIRT561795 PAWR pro-apoptotic WT1 regulator 2 2
MIRT567007 KLHL15 kelch like family member 15 2 2
MIRT569298 SURF6 surfeit 6 2 2
MIRT570606 MTRNR2L11 MT-RNR2-like 11 2 2
MIRT572888 ADCY2 adenylate cyclase 2 2 2
MIRT573119 ADAMTS18 ADAM metallopeptidase with thrombospondin type 1 motif 18 2 2
MIRT608332 ZNF670 zinc finger protein 670 2 6
MIRT614942 KCNK5 potassium two pore domain channel subfamily K member 5 2 2
MIRT615324 ERN1 endoplasmic reticulum to nucleus signaling 1 2 2
MIRT618441 ZNF800 zinc finger protein 800 2 2
MIRT620110 HARBI1 harbinger transposase derived 1 2 2
MIRT626008 ZNF517 zinc finger protein 517 2 2
MIRT626626 SLC30A6 solute carrier family 30 member 6 2 2
MIRT627842 POU3F1 POU class 3 homeobox 1 2 2
MIRT628386 CACNB2 calcium voltage-gated channel auxiliary subunit beta 2 2 2
MIRT629305 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT629864 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT630444 IDE insulin degrading enzyme 2 2
MIRT631854 PIGG phosphatidylinositol glycan anchor biosynthesis class G 2 2
MIRT633173 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT633477 ZNF724P zinc finger protein 724 2 2
MIRT634395 PLSCR1 phospholipid scramblase 1 2 2
MIRT635538 TRIM72 tripartite motif containing 72 2 2
MIRT635821 OPA3 OPA3, outer mitochondrial membrane lipid metabolism regulator 2 2
MIRT636169 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT636797 CYB5D1 cytochrome b5 domain containing 1 2 2
MIRT637952 IVD isovaleryl-CoA dehydrogenase 2 2
MIRT645136 HES2 hes family bHLH transcription factor 2 2 2
MIRT645667 ADK adenosine kinase 2 2
MIRT646148 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 2 2
MIRT647004 NCR3LG1 natural killer cell cytotoxicity receptor 3 ligand 1 2 2
MIRT648187 C2orf68 chromosome 2 open reading frame 68 2 2
MIRT650090 TERF2 telomeric repeat binding factor 2 2 2
MIRT650329 RTN2 reticulon 2 2 2
MIRT654224 RNF165 ring finger protein 165 2 2
MIRT654545 RAB1A RAB1A, member RAS oncogene family 2 2
MIRT656457 MAPK14 mitogen-activated protein kinase 14 2 2
MIRT656828 KLF8 Kruppel like factor 8 2 2
MIRT657112 ITPRIPL2 inositol 1,4,5-trisphosphate receptor interacting protein like 2 2 2
MIRT657930 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT659375 CREG2 cellular repressor of E1A stimulated genes 2 2 2
MIRT659833 CARHSP1 calcium regulated heat stable protein 1 2 2
MIRT662108 LACTB lactamase beta 2 4
MIRT662789 TBC1D25 TBC1 domain family member 25 2 2
MIRT669501 ARL3 ADP ribosylation factor like GTPase 3 2 2
MIRT669759 ZNF101 zinc finger protein 101 2 4
MIRT669800 GAN gigaxonin 2 2
MIRT670050 RPP14 ribonuclease P/MRP subunit p14 2 2
MIRT670299 RBBP4 RB binding protein 4, chromatin remodeling factor 2 2
MIRT670388 EMP2 epithelial membrane protein 2 2 2
MIRT672862 C22orf29 retrotransposon Gag like 10 2 2
MIRT672890 FXN frataxin 2 2
MIRT673210 C10orf76 chromosome 10 open reading frame 76 2 2
MIRT674001 KCNN3 potassium calcium-activated channel subfamily N member 3 2 2
MIRT674163 BLOC1S3 biogenesis of lysosomal organelles complex 1 subunit 3 2 2
MIRT674502 TIRAP TIR domain containing adaptor protein 2 2
MIRT675470 NUBPL nucleotide binding protein like 2 2
MIRT675671 TMOD2 tropomodulin 2 2 2
MIRT676006 CRKL CRK like proto-oncogene, adaptor protein 2 2
MIRT676074 TIMM50 translocase of inner mitochondrial membrane 50 2 2
MIRT676386 SEC24D SEC24 homolog D, COPII coat complex component 2 2
MIRT676764 SNX2 sorting nexin 2 2 2
MIRT676896 GABPB1 GA binding protein transcription factor beta subunit 1 2 2
MIRT676978 ZNF708 zinc finger protein 708 2 2
MIRT677236 C15orf40 chromosome 15 open reading frame 40 2 2
MIRT677369 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT677464 PDLIM3 PDZ and LIM domain 3 2 2
MIRT678081 EIF2A eukaryotic translation initiation factor 2A 2 2
MIRT678093 ATCAY ATCAY, caytaxin 2 2
MIRT678324 FBLIM1 filamin binding LIM protein 1 2 2
MIRT678417 ANKRD36 ankyrin repeat domain 36 2 2
MIRT678521 ZNF347 zinc finger protein 347 2 2
MIRT678700 TRIP11 thyroid hormone receptor interactor 11 2 2
MIRT678829 PDE6A phosphodiesterase 6A 2 2
MIRT679991 RUNDC1 RUN domain containing 1 2 2
MIRT680751 PSD4 pleckstrin and Sec7 domain containing 4 2 2
MIRT681249 ZNF383 zinc finger protein 383 2 2
MIRT681422 GTF3C6 general transcription factor IIIC subunit 6 2 2
MIRT681948 SLC19A3 solute carrier family 19 member 3 2 2
MIRT689278 C5AR2 complement component 5a receptor 2 2 2
MIRT690389 PARP15 poly(ADP-ribose) polymerase family member 15 2 2
MIRT691845 OSCAR osteoclast associated, immunoglobulin-like receptor 2 2
MIRT693863 IYD iodotyrosine deiodinase 2 2
MIRT696002 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 2
MIRT701930 MLLT1 MLLT1, super elongation complex subunit 2 2
MIRT702341 KLHL7 kelch like family member 7 2 2
MIRT703557 FKBP14 FK506 binding protein 14 2 2
MIRT705033 CACUL1 CDK2 associated cullin domain 1 2 2
MIRT706341 STAC2 SH3 and cysteine rich domain 2 2 2
MIRT709671 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT711212 EFHB EF-hand domain family member B 2 2
MIRT718342 PURA purine rich element binding protein A 2 2
MIRT722755 SIRPB2 signal regulatory protein beta 2 2 2
MIRT723535 NFATC2IP nuclear factor of activated T-cells 2 interacting protein 2 2
MIRT724498 BFAR bifunctional apoptosis regulator 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4680-5p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)

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