pre-miRNA Information
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
Mature miRNA hsa-miR-4640-5p
Sequence 9| UGGGCCAGGGAGCAGCUGGUGGG |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1392105945 7 dbSNP
rs939712790 9 dbSNP
rs762825841 15 dbSNP
rs71552023 20 dbSNP
rs1305909531 21 dbSNP
rs750017220 21 dbSNP
rs1375436057 23 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B32FZJ miR-4640 Safety Biomarker (SAF) Clinical/Experimental Data Expression lower Urine Quantitative polymerase chain reaction
Gene Information
Gene Symbol ATXN2   
Synonyms ATX2, SCA2, TNRC13
Description ataxin 2
Transcript NM_002973   
Expression
Putative miRNA Targets on ATXN2
3'UTR of ATXN2
(miRNA target sites are highlighted)
>ATXN2|NM_002973|3'UTR
   1 GGCTGCCCTGGAGGAACCGAAAGGCCAAATTCCCTCCTCCCTTCTACTGCTTCTACCAACTGGAAGCACAGAAAACTAGA
  81 ATTTCATTTATTTTGTTTTTAAAATATATATGTTGATTTCTTGTAACATCCAATAGGAATGCTAACAGTTCACTTGCAGT
 161 GGAAGATACTTGGACCGAGTAGAGGCATTTAGGAACTTGGGGGCTATTCCATAATTCCATATGCTGTTTCAGAGTCCCGC
 241 AGGTACCCCAGCTCTGCTTGCCGAAACTGGAAGTTATTTATTTTTTAATAACCCTTGAAAGTCATGAACACATCAGCTAG
 321 CAAAAGAAGTAACAAGAGTGATTCTTGCTGCTATTACTGCTAAAAAAAAAAAAAAAAAAAAATCAAGACTTGGAACGCCC
 401 TTTTACTAAACTTGACAAAGTTTCAGTAAATTCTTACCGTCAAACTGACGGATTATTATTTATAAATCAAGTTTGATGAG
 481 GTGATCACTGTCTACAGTGGTTCAACTTTTAAGTTAAGGGAAAAACTTTTACTTTGTAGATAATATAAAATAAAAACTTA
 561 AAAAAAATTTAAAAAATAAAAAAAGTTTTAAAAACTGAAAAAAAAAAA
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' ggGUGGUCGACGAGGGACCGGgu 5'
            | |||||| ||  || |||  
Target 5' taCCCCAGCT-CT-GCTTGCCga 3'
244 - 264 111.00 -22.10
2
miRNA  3' ggGUGGUCGACGAGGGACCGGGu 5'
            || ::|  | | |:||| || 
Target 5' tgCAGTGGAAGATACTTGGACCg 3'
155 - 177 109.00 -13.20
3
miRNA  3' ggguggUCGACGAGGGACCgggu 5'
                :||||  ||||||    
Target 5' ------GGCTG--CCCTGGagga 3'
1 - 15 101.00 -15.36
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30543130 7 COSMIC
COSN26465583 9 COSMIC
COSN1080549 11 COSMIC
COSN31505690 18 COSMIC
COSN30152089 49 COSMIC
COSN30499534 50 COSMIC
COSN30519869 80 COSMIC
COSN18747062 95 COSMIC
COSN21007807 197 COSMIC
COSN31579511 239 COSMIC
COSN31542503 263 COSMIC
COSN31485168 314 COSMIC
COSN32061887 362 COSMIC
COSN31596800 448 COSMIC
COSN26637046 468 COSMIC
COSN26573003 551 COSMIC
rs11348701 382 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs141600110 1 dbSNP
rs745432430 2 dbSNP
rs778382731 5 dbSNP
rs757254794 6 dbSNP
rs376658853 11 dbSNP
rs375359382 18 dbSNP
rs372412953 19 dbSNP
rs752500419 24 dbSNP
rs767667906 27 dbSNP
rs763583124 28 dbSNP
rs1245974951 36 dbSNP
rs1374158325 39 dbSNP
rs774613038 43 dbSNP
rs759777495 44 dbSNP
rs1393845256 49 dbSNP
rs751743550 51 dbSNP
rs375430831 56 dbSNP
rs763058339 66 dbSNP
rs1368614280 72 dbSNP
rs1167178992 73 dbSNP
rs773868096 79 dbSNP
rs1370468037 83 dbSNP
rs1424752622 85 dbSNP
rs1335605269 88 dbSNP
rs10661 95 dbSNP
rs771301346 96 dbSNP
rs1215606329 100 dbSNP
rs749052489 101 dbSNP
rs770285250 101 dbSNP
rs1423425514 107 dbSNP
rs1252635605 108 dbSNP
rs1184366839 111 dbSNP
rs769796175 112 dbSNP
rs777714896 112 dbSNP
rs762115985 115 dbSNP
rs777032616 120 dbSNP
rs538038973 123 dbSNP
rs1001459090 131 dbSNP
rs963166082 136 dbSNP
rs1422390964 137 dbSNP
rs1164857901 138 dbSNP
rs1354736150 149 dbSNP
rs753800860 149 dbSNP
rs1461544227 153 dbSNP
rs1166461979 158 dbSNP
rs1330400155 159 dbSNP
rs1016121249 170 dbSNP
rs1005628737 175 dbSNP
rs996816394 176 dbSNP
rs763808537 177 dbSNP
rs150319790 182 dbSNP
rs1047057175 198 dbSNP
rs1420700009 203 dbSNP
rs1175846381 204 dbSNP
rs1470000765 205 dbSNP
rs1235282792 206 dbSNP
rs1233832206 209 dbSNP
rs1040373022 210 dbSNP
rs1184169670 219 dbSNP
rs1004981165 221 dbSNP
rs1482507947 222 dbSNP
rs1187638963 225 dbSNP
rs1258906932 232 dbSNP
rs141258927 239 dbSNP
rs555358153 247 dbSNP
rs1416810812 262 dbSNP
rs1049611990 270 dbSNP
rs552206037 271 dbSNP
rs1170771999 275 dbSNP
rs901183152 278 dbSNP
rs1464418350 284 dbSNP
rs931187900 292 dbSNP
rs1040320670 297 dbSNP
rs1416545324 304 dbSNP
rs752377658 305 dbSNP
rs1045001694 316 dbSNP
rs942973776 317 dbSNP
rs1282132437 319 dbSNP
rs542542891 320 dbSNP
rs926093911 321 dbSNP
rs1298049714 327 dbSNP
rs191226454 329 dbSNP
rs917585912 333 dbSNP
rs1373700226 336 dbSNP
rs34618076 337 dbSNP
rs1486835873 339 dbSNP
rs1281097479 348 dbSNP
rs1242025347 353 dbSNP
rs543478848 353 dbSNP
rs945780634 353 dbSNP
rs1186589516 360 dbSNP
rs1421284244 361 dbSNP
rs1172561753 362 dbSNP
rs1452205510 362 dbSNP
rs913010867 362 dbSNP
rs1369852394 369 dbSNP
rs1316190238 377 dbSNP
rs1325956552 377 dbSNP
rs11348701 383 dbSNP
rs1290693029 383 dbSNP
rs1344500573 383 dbSNP
rs1431657381 383 dbSNP
rs1491363617 383 dbSNP
rs574744097 383 dbSNP
rs992497705 383 dbSNP
rs1442554375 384 dbSNP
rs1491163890 384 dbSNP
rs186620842 384 dbSNP
rs1397310833 387 dbSNP
rs1448072258 387 dbSNP
rs907553702 397 dbSNP
rs1157484730 398 dbSNP
rs1192639189 405 dbSNP
rs956365031 412 dbSNP
rs1400643356 416 dbSNP
rs768641797 418 dbSNP
rs1407239434 435 dbSNP
rs979573014 436 dbSNP
rs1161114436 437 dbSNP
rs565866101 438 dbSNP
rs767142167 439 dbSNP
rs979990347 449 dbSNP
rs963321307 450 dbSNP
rs746077387 455 dbSNP
rs1279356180 456 dbSNP
rs117066377 470 dbSNP
rs532249038 471 dbSNP
rs1288286497 480 dbSNP
rs1332090782 484 dbSNP
rs995301657 485 dbSNP
rs898348329 486 dbSNP
rs1469833278 493 dbSNP
rs1469521852 495 dbSNP
rs1179152194 496 dbSNP
rs1365108199 506 dbSNP
rs1232095645 513 dbSNP
rs1470366696 519 dbSNP
rs1178929686 531 dbSNP
rs1415542670 536 dbSNP
rs1461050085 546 dbSNP
rs1182047801 549 dbSNP
rs1165735038 552 dbSNP
rs576986079 560 dbSNP
rs1214931577 562 dbSNP
rs1408436529 567 dbSNP
rs1026115774 568 dbSNP
rs1336751741 568 dbSNP
rs1355377704 568 dbSNP
rs896440401 568 dbSNP
rs947979602 568 dbSNP
rs998284181 571 dbSNP
rs1286061402 577 dbSNP
rs1231856593 581 dbSNP
rs1346696941 584 dbSNP
rs1193747998 585 dbSNP
rs1271826110 585 dbSNP
rs1438225200 585 dbSNP
rs762184183 585 dbSNP
rs901146235 586 dbSNP
rs1206356699 590 dbSNP
rs1255391505 594 dbSNP
rs1474849233 595 dbSNP
rs1018289769 597 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Hela
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 GSM1048187. RNA binding protein: AGO2. Condition:Hela_AGO2_CLIP_control ...

- Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al., 2013, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ggGUGG-UCGACGAGG-G-ACCGGGu 5'
            :||| | |  | || | |||||| 
Target 5' -aUACCAACCCACCCCACAUGGCCCa 3'
1 - 25
Article - Xue Y; Ouyang K; Huang J; Zhou Y; Ouyang H; et al.
- Cell, 2013
The induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. Here, we report that repression of a single RNA binding polypyrimidine-tract-binding (PTB) protein, which occurs during normal brain development via the action of miR-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we show that PTB has a previously undocumented function in the regulation of microRNA functions, suppressing or enhancing microRNA targeting by competitive binding on target mRNA or altering local RNA secondary structure. A key event during neuronal induction is the relief of PTB-mediated blockage of microRNA action on multiple components of the REST complex, thereby derepressing a large array of neuronal genes, including miR-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. This converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.
LinkOut: [PMID: 23313552]
CLIP-seq Support 1 for dataset GSM1048187
Method / RBP HITS-CLIP / AGO2
Cell line / Condition Hela / Hela_AGO2_CLIP_control
Location of target site ENST00000550104.1 | 3UTR | auaccaacccaccccacauggcccacguaccucagg
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23313552 / GSE42701
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
87 hsa-miR-4640-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT100106 ABT1 activator of basal transcription 1 2 8
MIRT248144 LMBR1L limb development membrane protein 1 like 2 2
MIRT327062 KLHL15 kelch like family member 15 2 2
MIRT347231 GATAD2A GATA zinc finger domain containing 2A 2 2
MIRT450221 CENPN centromere protein N 2 2
MIRT451264 NDUFA11 NADH:ubiquinone oxidoreductase subunit A11 2 2
MIRT452701 C1orf226 chromosome 1 open reading frame 226 2 2
MIRT453212 CERS1 ceramide synthase 1 2 2
MIRT454822 POLR2J3 RNA polymerase II subunit J3 2 2
MIRT454883 RAD50 RAD50 double strand break repair protein 2 2
MIRT455783 TAF8 TATA-box binding protein associated factor 8 2 2
MIRT455858 TMEM254 transmembrane protein 254 2 2
MIRT457615 UPK3BL uroplakin 3B like 1 2 2
MIRT457822 ITPRIP inositol 1,4,5-trisphosphate receptor interacting protein 2 4
MIRT458344 NOC2L NOC2 like nucleolar associated transcriptional repressor 2 2
MIRT458376 ITM2C integral membrane protein 2C 2 2
MIRT458928 SAMD4B sterile alpha motif domain containing 4B 2 2
MIRT459066 WFIKKN2 WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 2 2
MIRT460138 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT460818 FSTL4 follistatin like 4 2 2
MIRT461285 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT462738 EFNB1 ephrin B1 2 2
MIRT464556 UBTF upstream binding transcription factor, RNA polymerase I 2 2
MIRT477910 DUSP2 dual specificity phosphatase 2 2 2
MIRT479073 CNNM4 cyclin and CBS domain divalent metal cation transport mediator 4 2 4
MIRT479534 CDC5L cell division cycle 5 like 2 4
MIRT485628 EEPD1 endonuclease/exonuclease/phosphatase family domain containing 1 2 2
MIRT489896 PPIC peptidylprolyl isomerase C 2 4
MIRT490737 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491201 MLLT1 MLLT1, super elongation complex subunit 2 4
MIRT492681 PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein 2 2
MIRT494593 ATG7 autophagy related 7 2 2
MIRT495061 PADI3 peptidyl arginine deiminase 3 2 4
MIRT496623 TMEM67 transmembrane protein 67 2 2
MIRT497177 ZBTB40 zinc finger and BTB domain containing 40 2 2
MIRT498217 TLN2 talin 2 2 2
MIRT498306 BCL11B B-cell CLL/lymphoma 11B 2 2
MIRT499668 NPHP3 nephrocystin 3 2 2
MIRT508080 ANKRD52 ankyrin repeat domain 52 2 2
MIRT509707 ANKRD23 ankyrin repeat domain 23 2 2
MIRT509841 FOS Fos proto-oncogene, AP-1 transcription factor subunit 2 2
MIRT512814 ARRDC2 arrestin domain containing 2 2 2
MIRT513353 SLIT1 slit guidance ligand 1 2 2
MIRT514293 FXYD5 FXYD domain containing ion transport regulator 5 2 2
MIRT516598 FAM89A family with sequence similarity 89 member A 2 4
MIRT516616 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT518348 CCL5 C-C motif chemokine ligand 5 2 2
MIRT520130 WSB1 WD repeat and SOCS box containing 1 2 2
MIRT522072 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT526461 OSBPL5 oxysterol binding protein like 5 2 2
MIRT528278 MBL2 mannose binding lectin 2 2 2
MIRT534844 RAB15 RAB15, member RAS oncogene family 2 4
MIRT542245 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT543299 ZNF585B zinc finger protein 585B 2 2
MIRT552456 ZNF410 zinc finger protein 410 2 2
MIRT553641 TJAP1 tight junction associated protein 1 2 2
MIRT557103 HOXA3 homeobox A3 2 2
MIRT570782 FANCA Fanconi anemia complementation group A 2 2
MIRT630912 ZMAT2 zinc finger matrin-type 2 2 2
MIRT631034 ZNF878 zinc finger protein 878 2 2
MIRT639017 AAK1 AP2 associated kinase 1 2 2
MIRT648596 ZYG11B zyg-11 family member B, cell cycle regulator 2 2
MIRT648939 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle 2 2
MIRT652834 TACO1 translational activator of cytochrome c oxidase I 2 2
MIRT659347 CSRP1 cysteine and glycine rich protein 1 2 2
MIRT664163 APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F 2 2
MIRT670511 ZSCAN22 zinc finger and SCAN domain containing 22 2 2
MIRT671246 TMEM41B transmembrane protein 41B 2 2
MIRT672120 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT672313 CD3D CD3d molecule 2 2
MIRT672543 BRMS1L breast cancer metastasis-suppressor 1 like 2 2
MIRT673036 SGPL1 sphingosine-1-phosphate lyase 1 2 2
MIRT673814 DARS aspartyl-tRNA synthetase 2 2
MIRT674858 GINM1 glycoprotein integral membrane 1 2 2
MIRT674970 SH3BP2 SH3 domain binding protein 2 2 2
MIRT675185 KIF1C kinesin family member 1C 2 2
MIRT675219 UGDH UDP-glucose 6-dehydrogenase 2 2
MIRT675558 MED16 mediator complex subunit 16 2 2
MIRT682566 EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 2 2
MIRT684640 PDE4C phosphodiesterase 4C 2 2
MIRT689722 ATXN2 ataxin 2 2 2
MIRT693594 SLC39A1 solute carrier family 39 member 1 2 2
MIRT704745 CDKN2B cyclin dependent kinase inhibitor 2B 2 2
MIRT712779 ZNF154 zinc finger protein 154 2 2
MIRT718118 OTOF otoferlin 2 2
MIRT720115 SAMD4A sterile alpha motif domain containing 4A 2 2
MIRT720275 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4640 Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Fluorouracil 3385 NSC19893 approved resistant High Pancreatic Cancer cell line (PANC-1)
hsa-mir-4640 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4640-5p Platinum 23939 sensitive High Ovarian Cancer tissue
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4640-5p Gemcitabine 60750 NSC613327 approved resistant High Pancreatic Cancer cell line (AsPC-1)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-4640-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4640-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4640-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4640-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-4640-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

Error report submission