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 ZMAT2   
Synonyms Ptg-12, Snu23
Description zinc finger matrin-type 2
Transcript NM_144723   
Expression
Putative miRNA Targets on ZMAT2
3'UTR of ZMAT2
(miRNA target sites are highlighted)
>ZMAT2|NM_144723|3'UTR
   1 GGCTTTCTGTGCTTGGCCTGACTTTGGCCTATGCTGGACCTAACTTTGCGTGTGTGTGTGTGTAGTAGGGGGTCATTTCT
  81 TTTTGGGTAATGGGAAAGTTCTTAAGAGTGTCAATGGGGAGGGATAGAGGGTGGGGGCTCATGGTTTCCCTCTACTTTGG
 161 GAGAGGGCACAGATTGCAGAGGTAATGCTGTGGCATATTGCTTCTGCCTCAGTGTATCACTGGAGTCACAGGACCCTGCC
 241 CACCTGAGTTCCCAATAAAGAAAAACCTCCCCTTCTGAGGCTGCTTTCCCAAAACTCCCCCTGCATCTTTATCTCTTCAT
 321 CTATCCCACCTCTTGTCTGAACATCCCACCTTTATCCTGTGTTCTGCCTTTGTTTTAATTTTAACTCATGTTCATCCTGC
 401 AACAGAAGCATTCTCTAGGTCCCAGTTTCCAGTTGATTGCATATCCTTGATCAGCCCTTTTTCCCATCCTGCCCTATGGT
 481 TCTCTAGCCACCTGTGCATGCATGTGTATTTCTGCCTGGTTCTATGGTGTGTGGATGTGTGTGCATGAATCTGTCATATA
 561 GAGGGGGTCCGAGCTGGAATCCTAGAGCATTGCTGCCCTGGGGCCTGATGTTCTTGGCTTCCTCAGAGCATGTAACAGGA
 641 AATTAAATGGGATGAGTGTTTGGTGTGGTTTGTGTCTGATGAGTTTTTTAACATTCAGGTGTAGATTGTTTCAGCTTCTC
 721 ATGTTTCATTTTCCTGAAGATTTATGTTTTTGTCTACCTTGTGAGCAGGCTTTTGGAAGAACCTGTTTGATGCAAAAAAG
 801 AAAATGAAAAACAAAACAAAAAATCCCCAAAACCTTATTATGGGAGCCCGTCGGTCTTAGAAGCTGTTTGACATGTATAA
 881 TAAATGGCATTGACTGGGCCTGTTTTACATTTGGTGAGAACATTCAAAAAAAAAAAAAAAAAA
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' --gGCTTTCTG-TGCTTGGCCTg 3'
1 - 20 123.00 -16.30
2
miRNA  3' ggguggucGACGAGGGACCGGGu 5'
                  :| || |||||::| 
Target 5' catgtgtaTTTCTGCCTGGTTCt 3'
501 - 523 123.00 -15.20
3
miRNA  3' ggGUGGUCGACG--AGGGA-CCGGGu 5'
            || |||  ||  ||:|| ||:|| 
Target 5' tgCAACAGAAGCATTCTCTAGGTCCc 3'
398 - 423 119.00 -18.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31492400 30 COSMIC
COSN30104694 37 COSMIC
COSN31592397 50 COSMIC
COSN24402023 63 COSMIC
COSN1083695 64 COSMIC
COSN14143582 80 COSMIC
COSN15235209 153 COSMIC
COSN18328481 239 COSMIC
COSN5158454 397 COSMIC
COSN31516451 414 COSMIC
COSN30543290 459 COSMIC
COSN30163265 480 COSMIC
COSN29461246 527 COSMIC
COSN21588994 530 COSMIC
COSN31548622 572 COSMIC
COSN31486204 671 COSMIC
COSN31515505 684 COSMIC
COSN28473248 690 COSMIC
COSN26537565 740 COSMIC
COSN18876105 769 COSMIC
COSN26465084 851 COSMIC
COSN5590562 878 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs370191105 3 dbSNP
rs768328648 7 dbSNP
rs1035937897 11 dbSNP
rs1362283783 14 dbSNP
rs1172277596 17 dbSNP
rs573295102 18 dbSNP
rs761606272 30 dbSNP
rs577155951 32 dbSNP
rs1187454893 34 dbSNP
rs762991993 35 dbSNP
rs1175507908 39 dbSNP
rs1467297727 43 dbSNP
rs1172762833 44 dbSNP
rs371033890 50 dbSNP
rs754400349 50 dbSNP
rs780532305 50 dbSNP
rs897997574 51 dbSNP
rs766532741 52 dbSNP
rs749630647 53 dbSNP
rs1288688902 54 dbSNP
rs1161057187 59 dbSNP
rs11542986 63 dbSNP
rs140468085 68 dbSNP
rs1282802554 73 dbSNP
rs75525728 76 dbSNP
rs76442552 77 dbSNP
rs1220384082 83 dbSNP
rs1345127587 86 dbSNP
rs1273867025 88 dbSNP
rs1163328435 90 dbSNP
rs1396083351 108 dbSNP
rs1438234334 109 dbSNP
rs1298634716 117 dbSNP
rs575822301 124 dbSNP
rs541475565 131 dbSNP
rs1377229116 137 dbSNP
rs540169014 138 dbSNP
rs1416192508 141 dbSNP
rs751219110 142 dbSNP
rs1392263251 144 dbSNP
rs546394098 145 dbSNP
rs1033714855 153 dbSNP
rs564482436 166 dbSNP
rs1315640425 169 dbSNP
rs912357767 194 dbSNP
rs112167203 196 dbSNP
rs528600785 203 dbSNP
rs1240800548 205 dbSNP
rs943952973 209 dbSNP
rs1239042347 211 dbSNP
rs960902906 215 dbSNP
rs1442490704 219 dbSNP
rs1277348967 223 dbSNP
rs992130309 233 dbSNP
rs1039594999 240 dbSNP
rs913700226 255 dbSNP
rs1319500763 268 dbSNP
rs1217719178 276 dbSNP
rs1359626359 277 dbSNP
rs1337102575 279 dbSNP
rs945222506 299 dbSNP
rs1252566548 300 dbSNP
rs1448755362 305 dbSNP
rs979126307 306 dbSNP
rs188336501 313 dbSNP
rs1336104844 319 dbSNP
rs925013481 324 dbSNP
rs932430294 326 dbSNP
rs368496698 329 dbSNP
rs1178664360 330 dbSNP
rs1171663199 331 dbSNP
rs549522200 355 dbSNP
rs1428275316 359 dbSNP
rs754474915 363 dbSNP
rs1049852874 367 dbSNP
rs912268826 386 dbSNP
rs553389769 388 dbSNP
rs1418402793 414 dbSNP
rs142158125 418 dbSNP
rs372429454 424 dbSNP
rs150778676 426 dbSNP
rs1040637392 432 dbSNP
rs897968026 442 dbSNP
rs998863088 447 dbSNP
rs993684520 453 dbSNP
rs573389624 457 dbSNP
rs1305553189 463 dbSNP
rs1314662156 466 dbSNP
rs1419970149 470 dbSNP
rs895966377 477 dbSNP
rs550671860 487 dbSNP
rs1002329302 488 dbSNP
rs1013601085 503 dbSNP
rs375853204 507 dbSNP
rs1400505499 508 dbSNP
rs775602004 522 dbSNP
rs1353097042 529 dbSNP
rs1167289126 531 dbSNP
rs1023206313 532 dbSNP
rs539312001 534 dbSNP
rs1440989843 538 dbSNP
rs973754262 545 dbSNP
rs1176239068 552 dbSNP
rs1479484368 554 dbSNP
rs960743687 571 dbSNP
rs1013889233 572 dbSNP
rs1242311506 578 dbSNP
rs1020844350 579 dbSNP
rs966619919 587 dbSNP
rs979219777 589 dbSNP
rs542403242 592 dbSNP
rs566325272 598 dbSNP
rs1231457331 601 dbSNP
rs1272639279 602 dbSNP
rs1371407599 612 dbSNP
rs533684132 620 dbSNP
rs912411341 625 dbSNP
rs943872453 626 dbSNP
rs953925487 628 dbSNP
rs559544272 634 dbSNP
rs1422109618 636 dbSNP
rs1380354608 654 dbSNP
rs1157677960 657 dbSNP
rs762943285 663 dbSNP
rs1268949590 669 dbSNP
rs1191465627 673 dbSNP
rs985228716 677 dbSNP
rs1480160394 684 dbSNP
rs1266558217 685 dbSNP
rs947409855 700 dbSNP
rs1043071750 705 dbSNP
rs1260106519 715 dbSNP
rs1238338024 721 dbSNP
rs6848 722 dbSNP
rs1387632654 724 dbSNP
rs1345243940 737 dbSNP
rs1301739212 741 dbSNP
rs11410 742 dbSNP
rs1041004788 743 dbSNP
rs139197618 745 dbSNP
rs544302949 746 dbSNP
rs1450974869 752 dbSNP
rs1378922621 753 dbSNP
rs1186595105 755 dbSNP
rs14803 771 dbSNP
rs1479934249 778 dbSNP
rs1057117709 783 dbSNP
rs896018895 789 dbSNP
rs1013081523 794 dbSNP
rs1488498169 794 dbSNP
rs1203379729 808 dbSNP
rs1484932324 815 dbSNP
rs768346688 818 dbSNP
rs1224337286 826 dbSNP
rs1323039156 829 dbSNP
rs1429890638 830 dbSNP
rs537870536 844 dbSNP
rs6849 851 dbSNP
rs532781700 853 dbSNP
rs899421521 854 dbSNP
rs995457004 866 dbSNP
rs1026669007 875 dbSNP
rs1403693828 877 dbSNP
rs950998592 879 dbSNP
rs542078134 888 dbSNP
rs1049251552 892 dbSNP
rs149960125 895 dbSNP
rs1372356122 905 dbSNP
rs1190902756 906 dbSNP
rs1425540888 907 dbSNP
rs1413536151 915 dbSNP
rs1292717157 925 dbSNP
rs1204345261 931 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 GSM1084044. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep3 HITS-CLIP data was present in GSM1084074. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_SantaCruzAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gggUGGUCGACGAGGGACCGGgu 5'
             :||| ||||  |||||||  
Target 5' ugaGCCA-CUGC-ACCUGGCC-- 3'
13 - 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]
CLIP-seq Support 1 for dataset GSM1084044
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep3
Location of target site ENST00000274712.3 | 3UTR | AUUACAGGCGUGAGCCACUGCACCUGGCCC
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 GSM1084074
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_SantaCruzAb
Location of target site ENST00000274712.3 | 3UTR | GGAUUACAGGCGUGAGCCACUGCACCUGGCC
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
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)

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