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 EIF4EBP1   
Synonyms 4E-BP1, 4EBP1, BP-1, PHAS-I
Description eukaryotic translation initiation factor 4E binding protein 1
Transcript NM_004095   
Expression
Putative miRNA Targets on EIF4EBP1
3'UTR of EIF4EBP1
(miRNA target sites are highlighted)
>EIF4EBP1|NM_004095|3'UTR
   1 AGCACCAGCCATCGTGTGGAGCACTACCAAGGGGCCCCTCAGGGCCTTCCTGGGAGGAGTCCCACCAGCCAGGCCTTATG
  81 AAAGTGATCATACTGGGCAGGCGTTGGCGTGGGGTCGGACACCCCAGCCCTTTCTCCCTCACTCAGGGCACCTGCCCCCT
 161 CCTCTTCGTGAACACCAGCAGATACCTCCTTGTGCCTCCACTGATGCAGGAGCTGCCACCCCAAGGGGAGTGACCCCTGC
 241 CAGCACACCCTGCAGCCAAGGGCCAGGAAGTGGACAAGAACGAACCCTTCCTTCCGAATGATCAGCAGTTCCAGCCCCTC
 321 GCTGCTGGGGGCGCAACCACCCCTTCCTTAGGTTGATGTGCTTGGGAAAGCTCCCTCCCCCTCCTTCCCCAAGAGAGGAA
 401 ATAAAAGCCACCTTCGCCCTAGGGCCAAGAAAAAAAAAAAAAAAAAAA
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' ggGUG-GUCGACGAGGGACCGGGu 5'
            ||| |||  ||  |||| ||| 
Target 5' ctCACTCAG-GGC-ACCTGCCCCc 3'
138 - 159 123.00 -21.20
2
miRNA  3' ggGUGGUCGAC----GAGGGAC-CGGGu 5'
            ||||||| |    ||||:|| |||: 
Target 5' aaCACCAGCAGATACCTCCTTGTGCCTc 3'
171 - 198 119.00 -26.10
3
miRNA  3' gggUGGUCGACGAGGGA--CCGGgu 5'
             :||| || | ||||  ||||  
Target 5' aaaGCCACCTTCGCCCTAGGGCCaa 3'
404 - 428 112.00 -24.50
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30101184 4 COSMIC
COSN30448291 7 COSMIC
COSN31500682 14 COSMIC
COSN2275028 15 COSMIC
COSN31522013 26 COSMIC
COSN26974811 35 COSMIC
COSN20076247 40 COSMIC
COSN30469974 43 COSMIC
COSN30153999 50 COSMIC
COSN30169026 62 COSMIC
COSN31597372 64 COSMIC
COSN24398204 68 COSMIC
COSN30501423 87 COSMIC
COSN9262003 93 COSMIC
COSN30508519 97 COSMIC
COSN20051283 102 COSMIC
COSN20076434 104 COSMIC
COSN30640028 109 COSMIC
COSN26974812 110 COSMIC
COSN28874594 126 COSMIC
COSN30169023 135 COSMIC
COSN24311295 138 COSMIC
COSN23017204 151 COSMIC
COSN14341747 168 COSMIC
COSN32062531 297 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs141363035 2 dbSNP
rs753941404 5 dbSNP
rs1478680945 6 dbSNP
rs561472705 8 dbSNP
rs780095361 12 dbSNP
rs746922076 13 dbSNP
rs201004052 14 dbSNP
rs371852717 15 dbSNP
rs1488065004 16 dbSNP
rs1268198138 17 dbSNP
rs1211697771 23 dbSNP
rs1464966790 27 dbSNP
rs376946135 30 dbSNP
rs1219713912 31 dbSNP
rs772901137 34 dbSNP
rs1320462493 35 dbSNP
rs755380413 35 dbSNP
rs1276646798 36 dbSNP
rs762401667 38 dbSNP
rs554780861 39 dbSNP
rs770837501 43 dbSNP
rs1451277699 45 dbSNP
rs770459886 50 dbSNP
rs1384562916 52 dbSNP
rs1278901625 54 dbSNP
rs936532992 55 dbSNP
rs1345357624 56 dbSNP
rs764105301 57 dbSNP
rs369166115 60 dbSNP
rs1467072694 64 dbSNP
rs907911557 65 dbSNP
rs892270208 69 dbSNP
rs372784811 72 dbSNP
rs940689319 84 dbSNP
rs1378415574 87 dbSNP
rs943895977 89 dbSNP
rs1201181912 96 dbSNP
rs565301877 98 dbSNP
rs1452438375 99 dbSNP
rs532528481 103 dbSNP
rs76259589 104 dbSNP
rs149709505 109 dbSNP
rs529896805 110 dbSNP
rs1256613068 113 dbSNP
rs1198393778 116 dbSNP
rs1048013311 117 dbSNP
rs766355477 118 dbSNP
rs551875202 119 dbSNP
rs1330023227 120 dbSNP
rs1465464009 124 dbSNP
rs1309302140 133 dbSNP
rs1448963186 134 dbSNP
rs1374546144 137 dbSNP
rs1330499298 138 dbSNP
rs1470124634 141 dbSNP
rs1332391532 143 dbSNP
rs1004395543 144 dbSNP
rs1404005217 145 dbSNP
rs1174550747 146 dbSNP
rs1464691022 147 dbSNP
rs1016291380 155 dbSNP
rs960216692 161 dbSNP
rs569709066 164 dbSNP
rs1048925 165 dbSNP
rs947353316 168 dbSNP
rs1443363525 169 dbSNP
rs1281103699 174 dbSNP
rs1198399475 175 dbSNP
rs1343810066 183 dbSNP
rs536961665 184 dbSNP
rs28624549 187 dbSNP
rs1241670762 191 dbSNP
rs1351509972 193 dbSNP
rs751488066 197 dbSNP
rs570138233 198 dbSNP
rs1448593173 200 dbSNP
rs1342066352 201 dbSNP
rs534301662 206 dbSNP
rs1007856995 214 dbSNP
rs1394551257 215 dbSNP
rs1375056784 218 dbSNP
rs1159397856 219 dbSNP
rs566483688 229 dbSNP
rs1158594353 233 dbSNP
rs899557409 235 dbSNP
rs754838448 237 dbSNP
rs1441550537 238 dbSNP
rs1263453776 240 dbSNP
rs1218262370 247 dbSNP
rs1350879576 253 dbSNP
rs1284627372 258 dbSNP
rs1228851745 259 dbSNP
rs574471391 266 dbSNP
rs1358344727 268 dbSNP
rs541520118 270 dbSNP
rs988043932 271 dbSNP
rs11545133 273 dbSNP
rs555160609 282 dbSNP
rs1199054375 283 dbSNP
rs1317686533 286 dbSNP
rs1406507449 289 dbSNP
rs1416577392 291 dbSNP
rs1161900973 293 dbSNP
rs1475089940 296 dbSNP
rs1259678081 297 dbSNP
rs1195426741 300 dbSNP
rs1041308745 308 dbSNP
rs1261889168 309 dbSNP
rs1221636498 313 dbSNP
rs1453321984 316 dbSNP
rs1287647893 318 dbSNP
rs1467135848 318 dbSNP
rs921112776 322 dbSNP
rs1266829687 324 dbSNP
rs1279809574 326 dbSNP
rs1048934 333 dbSNP
rs1338678276 334 dbSNP
rs1269738046 336 dbSNP
rs1437278345 339 dbSNP
rs1015127099 340 dbSNP
rs1322166666 342 dbSNP
rs1461335156 358 dbSNP
rs1401521951 359 dbSNP
rs1173235045 363 dbSNP
rs1371566857 365 dbSNP
rs1476665002 374 dbSNP
rs1048146783 377 dbSNP
rs1418343566 378 dbSNP
rs888102587 381 dbSNP
rs762244825 382 dbSNP
rs1244423041 383 dbSNP
rs1220777284 387 dbSNP
rs78978523 388 dbSNP
rs1458131498 389 dbSNP
rs1259803629 391 dbSNP
rs1196510135 392 dbSNP
rs981378722 393 dbSNP
rs544157525 394 dbSNP
rs371690517 396 dbSNP
rs958841043 397 dbSNP
rs1378271284 408 dbSNP
rs896090200 412 dbSNP
rs1464396004 416 dbSNP
rs567241096 417 dbSNP
rs1023515020 420 dbSNP
rs1415782285 429 dbSNP
rs1422490834 430 dbSNP
rs1041656814 431 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293/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 GSM1067870. RNA binding protein: AGO2. Condition:Ago2 IP-seq (mitotic cells) ...

- Kishore S; Gruber AR; Jedlinski DJ; Syed et al., 2013, Genome biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ggguggucgacgagggaCCGGGu 5'
                           ||||| 
Target 5' -----------------GGCCCa 3'
1 - 6
Article - Kishore S; Gruber AR; Jedlinski DJ; Syed et al.
- Genome biology, 2013
BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
LinkOut: [PMID: 23706177]
CLIP-seq Support 1 for dataset GSM1067870
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293/HeLa / Ago2 IP-seq (mitotic cells)
Location of target site ENST00000338825.4 | 3UTR | GGCCCAGGCUGGAGUGCAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23706177 / GSE43666
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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