pre-miRNA Information
pre-miRNA hsa-mir-655   
Genomic Coordinates chr14: 101049550 - 101049646
Synonyms MIRN655, hsa-mir-655, MIR655
Description Homo sapiens miR-655 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-655-5p
Sequence 23| AGAGGUUAUCCGUGUUAUGUUC |44
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs766575622 4 dbSNP
rs754023562 5 dbSNP
rs757713353 10 dbSNP
rs369862924 11 dbSNP
rs552601004 12 dbSNP
rs753191773 14 dbSNP
rs569206109 15 dbSNP
rs373094888 18 dbSNP
rs778280798 22 dbSNP
Putative Targets

Gene Information
Gene Symbol ZC3HAV1L   
Synonyms C7orf39
Description zinc finger CCCH-type containing, antiviral 1 like
Transcript NM_080660   
Expression
Putative miRNA Targets on ZC3HAV1L
3'UTR of ZC3HAV1L
(miRNA target sites are highlighted)
>ZC3HAV1L|NM_080660|3'UTR
   1 AGAAGATGGAAAAGGAGAAAATGTCCTTTTGGAAGAATACATTTGGGCATGGGTGGTTGGGGATGGGGTGGGACATTGAA
  81 CAGGCAAAGAGAGGCTAAAATTGAGTGCAGATGGGGCTAGTCCAGGGCAAGTGCTGAAGATGGCAGCTGCTATCTGCAGC
 161 TCCTAGGTGCTTTCCTCAGGCTGGGTAGATGGAGCTCTGCTGACTTCTGTGGTCCACCATTGTTTTTCTATCAATTTATA
 241 TTGTGGCAATCCTAGAGTACTTTGCACTCATTTTTTTTTTTCACTTAATATTGTCTCATAAGCATCTTTCTATATTTGTT
 321 CACATCGTACATAATCATGTTTTTGCACAGATACATTAATATTATCATAGTTTGTTTAACTACTTGGCTTTTTCTAACAG
 401 TTTTTTTTTTTGAGATGGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGACGTGATCTCGGCTCACTGCAGCCTTGACT
 481 TCCTGGGCTCAAGTGATCATCCCACCTCAGCCTCCTGAGTAGCTGGGACTACAGGTATGCACCACGACCAGCTAATTTTT
 561 TGTATTTTTTTTTTGTAGAGAGGGTATTTTGCCATGTTGCCCAGGCTAGTCTTGAACTCCTGGGCTCAAGCGATCTGCCT
 641 GCTTCAGCCTCCCAGAGTGCTAGGATTACAGGCATGAGCCACTGCACCCAGCCTCTTAACAAATTTTGAATATAACTCCT
 721 GTCTTAAAATCTGCAGAATATTGAATTTTTCCAGCTATTTTTTACTTTTGCTTAGCTTATAGATGCTAAAGGATACTGTC
 801 ATTTGCATTTTTAAAAATATATGTATGAGTGAATAGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 881 AAAAAAA
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' cuUGUAUUGUGCCUAUUGGAGa 5'
            |:: |:| | | |:||:|| 
Target 5' agATGGAGCTCTGCTGACTTCt 3'
187 - 208 124.00 -9.51
2
miRNA  3' cuUGU-AUUGUGCCUAUUGGAGa 5'
            :|| |:||    :|:|:||| 
Target 5' gtGCAGTGAC----GTGATCTCg 3'
443 - 461 114.00 -8.90
3
miRNA  3' cuuGUAUUGUGCCUAUUGGAGa 5'
             ||||:: :|  ||||: | 
Target 5' tatCATAGTTTGTTTAACTACt 3'
363 - 384 111.00 -7.70
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30510389 21 COSMIC
COSN19121951 25 COSMIC
COSN27005549 27 COSMIC
COSN27005550 27 COSMIC
COSN27005551 56 COSMIC
COSN30537309 72 COSMIC
COSN27005552 78 COSMIC
COSN30527012 192 COSMIC
COSN20104862 270 COSMIC
COSN27589700 271 COSMIC
COSN28490554 564 COSMIC
COSN6353940 586 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1376637662 1 dbSNP
rs947907641 7 dbSNP
rs765419069 11 dbSNP
rs1336542248 14 dbSNP
rs781634462 17 dbSNP
rs759784808 20 dbSNP
rs111891533 31 dbSNP
rs894983722 37 dbSNP
rs556361392 41 dbSNP
rs771009734 43 dbSNP
rs115015323 44 dbSNP
rs1180234812 45 dbSNP
rs773656153 48 dbSNP
rs939267774 49 dbSNP
rs1245749767 51 dbSNP
rs532924358 56 dbSNP
rs867239563 63 dbSNP
rs150537133 68 dbSNP
rs923835216 81 dbSNP
rs977813485 84 dbSNP
rs77941163 86 dbSNP
rs915034411 90 dbSNP
rs115752120 94 dbSNP
rs1400454685 103 dbSNP
rs1370434817 104 dbSNP
rs953760331 105 dbSNP
rs1029131696 110 dbSNP
rs141661116 116 dbSNP
rs1227927738 126 dbSNP
rs112444031 127 dbSNP
rs1015580898 131 dbSNP
rs551368712 136 dbSNP
rs946719068 137 dbSNP
rs1467678895 145 dbSNP
rs1192250748 164 dbSNP
rs1264515397 177 dbSNP
rs1429412112 178 dbSNP
rs1409835306 193 dbSNP
rs1371757622 208 dbSNP
rs913879425 214 dbSNP
rs1165978954 215 dbSNP
rs189911848 216 dbSNP
rs550650377 228 dbSNP
rs939425157 229 dbSNP
rs1027619024 230 dbSNP
rs1012346505 231 dbSNP
rs757123559 233 dbSNP
rs928510353 234 dbSNP
rs767975062 239 dbSNP
rs1294570607 257 dbSNP
rs1338194753 263 dbSNP
rs562662249 265 dbSNP
rs1234722320 266 dbSNP
rs1257038935 266 dbSNP
rs542739746 267 dbSNP
rs1484374515 270 dbSNP
rs1238069907 271 dbSNP
rs76876234 271 dbSNP
rs1188866842 282 dbSNP
rs1486470190 282 dbSNP
rs369793399 282 dbSNP
rs879880075 282 dbSNP
rs969831772 283 dbSNP
rs1474228980 290 dbSNP
rs1161394535 299 dbSNP
rs1056334824 300 dbSNP
rs1023318672 301 dbSNP
rs939153378 303 dbSNP
rs1259978273 310 dbSNP
rs1358337816 310 dbSNP
rs1293451817 321 dbSNP
rs902460859 327 dbSNP
rs76416666 329 dbSNP
rs560777662 330 dbSNP
rs374018128 337 dbSNP
rs137891636 339 dbSNP
rs185983316 346 dbSNP
rs932422466 352 dbSNP
rs145210962 353 dbSNP
rs1212050476 355 dbSNP
rs1257007727 365 dbSNP
rs1484807395 369 dbSNP
rs1179243930 370 dbSNP
rs1408777709 372 dbSNP
rs10265929 387 dbSNP
rs1158235908 389 dbSNP
rs1439467323 392 dbSNP
rs576179189 401 dbSNP
rs1173503491 402 dbSNP
rs908157689 408 dbSNP
rs1044387918 412 dbSNP
rs1445314107 412 dbSNP
rs373451520 412 dbSNP
rs899968505 412 dbSNP
rs1299580550 414 dbSNP
rs1011139231 422 dbSNP
rs1390350626 423 dbSNP
rs984113653 427 dbSNP
rs1417536550 428 dbSNP
rs1163141826 431 dbSNP
rs1235745247 436 dbSNP
rs1280060855 437 dbSNP
rs952296622 439 dbSNP
rs1027674781 440 dbSNP
rs1310855396 443 dbSNP
rs866135024 443 dbSNP
rs1012235252 447 dbSNP
rs1257206423 452 dbSNP
rs1176672961 453 dbSNP
rs1052384325 456 dbSNP
rs1456537626 458 dbSNP
rs777541847 460 dbSNP
rs959472076 465 dbSNP
rs111743133 469 dbSNP
rs1412570667 472 dbSNP
rs1270974400 483 dbSNP
rs1354760857 485 dbSNP
rs1440757787 485 dbSNP
rs143088993 487 dbSNP
rs1442245259 501 dbSNP
rs902345072 503 dbSNP
rs1303339496 507 dbSNP
rs1365878201 510 dbSNP
rs1045099913 523 dbSNP
rs1273906769 525 dbSNP
rs948580518 532 dbSNP
rs1197054772 535 dbSNP
rs1275090104 536 dbSNP
rs915729916 537 dbSNP
rs112290712 542 dbSNP
rs1246089521 543 dbSNP
rs1476882680 545 dbSNP
rs536005983 546 dbSNP
rs1188065990 550 dbSNP
rs1420037245 551 dbSNP
rs1409008177 562 dbSNP
rs1168148203 564 dbSNP
rs77991415 565 dbSNP
rs1011251016 567 dbSNP
rs1461535500 568 dbSNP
rs1325740310 570 dbSNP
rs565459142 571 dbSNP
rs1433566444 575 dbSNP
rs893702696 575 dbSNP
rs962653088 575 dbSNP
rs1221544232 577 dbSNP
rs547042386 580 dbSNP
rs1295376366 592 dbSNP
rs1335509444 594 dbSNP
rs1213151607 595 dbSNP
rs769430504 596 dbSNP
rs1449781384 601 dbSNP
rs1217949207 603 dbSNP
rs1242457124 614 dbSNP
rs192029353 616 dbSNP
rs1419575911 617 dbSNP
rs1475215648 619 dbSNP
rs1390117542 620 dbSNP
rs112889923 622 dbSNP
rs1405041979 623 dbSNP
rs1388033018 624 dbSNP
rs1292145802 625 dbSNP
rs1402919119 631 dbSNP
rs1319610398 632 dbSNP
rs1459818533 635 dbSNP
rs1398575103 636 dbSNP
rs1314930002 641 dbSNP
rs1040768986 642 dbSNP
rs113856201 650 dbSNP
rs35318154 669 dbSNP
rs1282500710 671 dbSNP
rs1352988270 672 dbSNP
rs1225377646 691 dbSNP
rs908044388 693 dbSNP
rs768762390 702 dbSNP
rs1158699145 703 dbSNP
rs746889256 718 dbSNP
rs952420993 719 dbSNP
rs779966544 725 dbSNP
rs1366178294 726 dbSNP
rs754470649 745 dbSNP
rs537825870 755 dbSNP
rs115731935 758 dbSNP
rs549056439 762 dbSNP
rs906521852 764 dbSNP
rs1265255670 768 dbSNP
rs1211392422 770 dbSNP
rs1175903548 776 dbSNP
rs1376519152 783 dbSNP
rs1414370216 788 dbSNP
rs1337563180 795 dbSNP
rs959356426 800 dbSNP
rs116354985 813 dbSNP
rs1213950730 819 dbSNP
rs1352878081 823 dbSNP
rs1237948704 829 dbSNP
rs980289644 831 dbSNP
rs1348383257 836 dbSNP
rs187276264 839 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' cuuGUAUUGUGCCUAUUGGAGa 5'
             |||  |||  |||||||| 
Target 5' ucuCAUCUCAC-CAUAACCUCc 3'
11 - 31
2
miRNA  3' cuuguauugugccUAUUGgaga 5'
                       ||::|    
Target 5' ------------aAUGGCgcga 3'
1 - 10
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000275766.1 | 3UTR | AAUGGCGCGAUCUCAUCUCACCAUAACCUCCGCCUCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
91 hsa-miR-655-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT080691 KIAA1468 KIAA1468 2 2
MIRT095086 SEC24A SEC24 homolog A, COPII coat complex component 2 4
MIRT122450 SMIM13 small integral membrane protein 13 2 2
MIRT214635 SMAD5 SMAD family member 5 2 4
MIRT268267 CCND1 cyclin D1 2 2
MIRT312418 GRPEL2 GrpE like 2, mitochondrial 2 2
MIRT329008 DSTN destrin, actin depolymerizing factor 2 2
MIRT329824 PDCD4 programmed cell death 4 2 4
MIRT389635 LRRC58 leucine rich repeat containing 58 2 6
MIRT443969 FAM198B family with sequence similarity 198 member B 2 2
MIRT444080 C12orf73 chromosome 12 open reading frame 73 2 2
MIRT444886 TMEM196 transmembrane protein 196 2 2
MIRT445506 CRNKL1 crooked neck pre-mRNA splicing factor 1 2 4
MIRT446292 ACSL3 acyl-CoA synthetase long chain family member 3 2 2
MIRT446462 THAP1 THAP domain containing 1 2 2
MIRT446472 THUMPD3 THUMP domain containing 3 2 2
MIRT447413 MED21 mediator complex subunit 21 2 2
MIRT447491 KIAA1715 lunapark, ER junction formation factor 2 2
MIRT448965 CDADC1 cytidine and dCMP deaminase domain containing 1 2 2
MIRT449602 INIP INTS3 and NABP interacting protein 2 2
MIRT449607 PRPF4 pre-mRNA processing factor 4 2 2
MIRT449737 TAB2 TGF-beta activated kinase 1/MAP3K7 binding protein 2 2 2
MIRT451668 KRT8 keratin 8 2 4
MIRT452424 QDPR quinoid dihydropteridine reductase 2 2
MIRT455187 AGTRAP angiotensin II receptor associated protein 2 2
MIRT456059 SLC25A28 solute carrier family 25 member 28 2 2
MIRT456488 SERAC1 serine active site containing 1 2 2
MIRT456631 ARMCX6 armadillo repeat containing, X-linked 6 2 2
MIRT459621 SLC25A33 solute carrier family 25 member 33 2 2
MIRT461162 SLC11A2 solute carrier family 11 member 2 2 4
MIRT461990 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 2 2
MIRT463149 ZNF385A zinc finger protein 385A 2 4
MIRT463465 ZC3HAV1L zinc finger CCCH-type containing, antiviral 1 like 2 2
MIRT463801 XPOT exportin for tRNA 2 2
MIRT464010 WDR26 WD repeat domain 26 2 2
MIRT465302 TRIB1 tribbles pseudokinase 1 2 2
MIRT468837 RRM2 ribonucleotide reductase regulatory subunit M2 2 2
MIRT469132 RNF126 ring finger protein 126 2 2
MIRT469244 RHOB ras homolog family member B 2 2
MIRT472414 NCKAP1 NCK associated protein 1 2 2
MIRT472432 NCBP2 nuclear cap binding protein subunit 2 2 2
MIRT472808 MTMR12 myotubularin related protein 12 2 2
MIRT477893 DVL3 dishevelled segment polarity protein 3 2 4
MIRT477963 DPM2 dolichyl-phosphate mannosyltransferase subunit 2, regulatory 2 2
MIRT479258 CHSY1 chondroitin sulfate synthase 1 2 2
MIRT479718 CCNF cyclin F 2 2
MIRT480231 C9orf41 carnosine N-methyltransferase 1 2 2
MIRT482600 ABHD14B abhydrolase domain containing 14B 2 2
MIRT483096 TFPI tissue factor pathway inhibitor 2 2
MIRT484644 TBC1D5 TBC1 domain family member 5 2 4
MIRT488899 CLDND1 claudin domain containing 1 2 2
MIRT491954 VPS52 VPS52, GARP complex subunit 2 2
MIRT496937 LBR lamin B receptor 2 2
MIRT498546 TMEM30B transmembrane protein 30B 2 2
MIRT501778 NRBF2 nuclear receptor binding factor 2 2 6
MIRT516286 DBT dihydrolipoamide branched chain transacylase E2 2 2
MIRT516351 GABPB1 GA binding protein transcription factor beta subunit 1 2 2
MIRT516751 ZNF100 zinc finger protein 100 2 2
MIRT517939 ZNF431 zinc finger protein 431 2 4
MIRT518295 ZNF514 zinc finger protein 514 2 4
MIRT518515 CASP10 caspase 10 2 2
MIRT519017 NOA1 nitric oxide associated 1 2 2
MIRT519171 SCO1 SCO1, cytochrome c oxidase assembly protein 2 2
MIRT519470 SPTLC2 serine palmitoyltransferase long chain base subunit 2 2 2
MIRT521029 SLC30A5 solute carrier family 30 member 5 2 2
MIRT521251 SAMD8 sterile alpha motif domain containing 8 2 2
MIRT521682 PRKAR2A protein kinase cAMP-dependent type II regulatory subunit alpha 2 2
MIRT529386 SKP1 S-phase kinase associated protein 1 2 2
MIRT545507 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT549655 RSL1D1 ribosomal L1 domain containing 1 2 2
MIRT551041 CTSB cathepsin B 2 4
MIRT551441 ZNF490 zinc finger protein 490 2 4
MIRT554778 RHEBP1 RHEB pseudogene 1 2 4
MIRT565793 SEC14L5 SEC14 like lipid binding 5 2 2
MIRT566727 MSL2 MSL complex subunit 2 2 2
MIRT574668 HNRNPDL heterogeneous nuclear ribonucleoprotein D like 2 2
MIRT610128 DENND5B DENN domain containing 5B 2 2
MIRT624919 FBXW2 F-box and WD repeat domain containing 2 2 2
MIRT641830 TRIM71 tripartite motif containing 71 2 2
MIRT662165 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT667150 NRXN3 neurexin 3 2 2
MIRT689085 ADNP2 ADNP homeobox 2 2 2
MIRT696322 DCAF15 DDB1 and CUL4 associated factor 15 2 2
MIRT699062 SNX4 sorting nexin 4 2 2
MIRT703229 GOLGA1 golgin A1 2 2
MIRT705743 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT706087 HNRNPU heterogeneous nuclear ribonucleoprotein U 2 2
MIRT709288 MAPK8IP2 mitogen-activated protein kinase 8 interacting protein 2 2 2
MIRT711457 RNF145 ring finger protein 145 2 2
MIRT714708 PPP3CC protein phosphatase 3 catalytic subunit gamma 2 2
MIRT719871 CYP4F11 cytochrome P450 family 4 subfamily F member 11 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-655 Gefitinib approved 123631 Quantitative real-time PCR lung adenocarcinoma cells 24258346 2014 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-655 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-mir-655 Androstenedione 6128 NSC9563 resistant cell line (MCF-7)
hsa-mir-655 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-655-5p Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-655-5p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-655-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-655-5p Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)

Error report submission