pre-miRNA Information
pre-miRNA hsa-mir-4260   
Genomic Coordinates chr1: 209623444 - 209623510
Description Homo sapiens miR-4260 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4260
Sequence 11| CUUGGGGCAUGGAGUCCCA |29
Evidence Experimental
Experiments SOLiD
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSM7908770 6 COSMIC
COSN30117883 7 COSMIC
COSN26730871 12 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs372999583 2 dbSNP
rs1367351910 8 dbSNP
rs1266505194 15 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol POMGNT1   
Synonyms GNTI.2, GnT I.2, LGMD2O, MEB, MGAT1.2, RP76, gnT-I.2
Description protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)
Transcript NM_017739   
Expression
Putative miRNA Targets on POMGNT1
3'UTR of POMGNT1
(miRNA target sites are highlighted)
>POMGNT1|NM_017739|3'UTR
   1 GACCTCCTCCAGGACCCTGCGGGGCTGGGTACTGTGTACCCCCAGGCTGGCTAGCCCTTCCCTCCATCCTGTAGGATTTT
  81 GTAGATGCTGGTAGGGGCTGGGGCTACCTTGTTTTTAACATGAGACTTAATTACTAACTCCAAGGGGAGGGTTCCCCTGC
 161 TCCAACACCCCGTTCCTGAGTTAAAAGTCTATTTATTTACTTCCTTGTTGGAGAAGGGCAGGAGAGTACCTGGGAATCAT
 241 TACGATCCCTAGCAGCTCATCCTGCCCTTTGAATACCCTCACTTTCCAGGCCTGGCTCAGAATCTAACCTATTTATTGAC
 321 TGTCCTGAGGGCCTTGAAAACAGGCCGAACCTGGAGGGCCTGGATTTCTTTTTGGGCTGGAATGCTGCCCTGAGGGTGGG
 401 GCTGGCTCTTACTCAGGAAACTGCTGTGCCCAACCCATGGACAGGCCCAGCTGGGGCCCACATGCTGACACAGACTCACT
 481 CAGAGACCCTTAGACACTGGACCAGGCCTCCTCTCAGCCTTCTCTTTGTCCAGATTTCCAAAGCTGGATAAGTTGGTCAT
 561 TGATTAAAAAAGGAGAAGCCCTCTGGGGAAAAAAAAAAAAAAAAAA
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' acCCUGA-GGUACGGGGUUc 5'
            ||::| || |||:|||| 
Target 5' gaGGGTTCCCCTGCTCCAAc 3'
147 - 166 145.00 -18.90
2
miRNA  3' acCCUGAGGUACGGGGUUc 5'
            ||| | | |||||::| 
Target 5' ctGGAATGC-TGCCCTGAg 3'
377 - 394 124.00 -15.60
3
miRNA  3' acccUGA-GGUACGGGGUuc 5'
              ||| |::||||| |  
Target 5' ggaaACTGCTGTGCCCAAcc 3'
416 - 435 107.00 -12.56
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
989704 2 ClinVar
554892 11 ClinVar
978968 12 ClinVar
557754 34 ClinVar
873654 34 ClinVar
876537 207 ClinVar
876536 221 ClinVar
558144 362 ClinVar
555405 406 ClinVar
297532 451 ClinVar
1209779 457 ClinVar
554758 499 ClinVar
550470 500 ClinVar
554543 514 ClinVar
553241 531 ClinVar
COSM8188185 17 COSMIC
COSM8068056 21 COSMIC
COSM7740324 22 COSMIC
COSM6282980 24 COSMIC
COSM1159339 25 COSMIC
COSM8794562 27 COSMIC
COSN30513722 239 COSMIC
COSN30108334 243 COSMIC
COSN30488609 247 COSMIC
COSN30511517 249 COSMIC
COSM8407293 288 COSMIC
COSM7813078 289 COSMIC
COSM284146 313 COSMIC
COSM9812383 316 COSMIC
COSM7634942 346 COSMIC
COSM8420811 346 COSMIC
COSM8781353 347 COSMIC
COSM7904191 359 COSMIC
COSM7904244 360 COSMIC
COSM9654897 362 COSMIC
COSM6752602 375 COSMIC
COSM1644906 388 COSMIC
COSM7095097 392 COSMIC
COSM9325556 394 COSMIC
COSM7316608 395 COSMIC
COSM3805433 424 COSMIC
COSM3985112 434 COSMIC
COSM7936249 453 COSMIC
COSM3805432 467 COSMIC
COSM3690290 499 COSMIC
COSM7430369 522 COSMIC
COSM8044007 533 COSMIC
COSN30190047 562 COSMIC
COSN26989910 566 COSMIC
COSN30746601 566 COSMIC
COSN30520435 585 COSMIC
COSN30519489 586 COSMIC
COSN31500455 587 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1389865857 1 dbSNP
rs1188540095 2 dbSNP
rs773221879 10 dbSNP
rs772014576 11 dbSNP
rs780919404 11 dbSNP
rs1391347556 12 dbSNP
rs1451672762 13 dbSNP
rs1456713621 17 dbSNP
rs1171203772 19 dbSNP
rs761660715 20 dbSNP
rs773913718 21 dbSNP
rs374145749 22 dbSNP
rs1385873142 24 dbSNP
rs748808819 25 dbSNP
rs1186619711 32 dbSNP
rs200540049 34 dbSNP
rs949105013 39 dbSNP
rs1470155625 42 dbSNP
rs1274088437 45 dbSNP
rs747530937 46 dbSNP
rs1206742676 48 dbSNP
rs1344570064 49 dbSNP
rs778207309 51 dbSNP
rs758795805 53 dbSNP
rs753078397 61 dbSNP
rs142268597 62 dbSNP
rs755221193 64 dbSNP
rs1265055036 81 dbSNP
rs980591079 86 dbSNP
rs1360193799 87 dbSNP
rs1208220478 88 dbSNP
rs989497933 91 dbSNP
rs1249129038 101 dbSNP
rs1291141254 108 dbSNP
rs1244051981 120 dbSNP
rs956330556 148 dbSNP
rs770263857 156 dbSNP
rs1033658109 162 dbSNP
rs978902686 171 dbSNP
rs186950672 175 dbSNP
rs1478140884 177 dbSNP
rs1270532943 178 dbSNP
rs954178455 187 dbSNP
rs1429822916 195 dbSNP
rs1409355569 199 dbSNP
rs1324502482 200 dbSNP
rs546045840 200 dbSNP
rs1304827822 218 dbSNP
rs181362801 221 dbSNP
rs1364331772 232 dbSNP
rs998223479 234 dbSNP
rs1322611013 238 dbSNP
rs564610096 243 dbSNP
rs781694733 244 dbSNP
rs756213466 250 dbSNP
rs1033194400 256 dbSNP
rs750417663 258 dbSNP
rs1209811170 267 dbSNP
rs1390431410 276 dbSNP
rs1015582050 278 dbSNP
rs553802144 279 dbSNP
rs1353431801 280 dbSNP
rs770665651 285 dbSNP
rs1208631991 287 dbSNP
rs1267300934 297 dbSNP
rs1426731829 302 dbSNP
rs370793676 310 dbSNP
rs1167968826 320 dbSNP
rs774184831 322 dbSNP
rs1242690288 324 dbSNP
rs1195211075 325 dbSNP
rs1449694342 329 dbSNP
rs1266355905 333 dbSNP
rs1210082344 337 dbSNP
rs368285518 343 dbSNP
rs1271861128 344 dbSNP
rs762671303 346 dbSNP
rs746679629 347 dbSNP
rs769320607 350 dbSNP
rs745346713 353 dbSNP
rs11552406 356 dbSNP
rs1376441690 357 dbSNP
rs1330908649 358 dbSNP
rs1308180916 359 dbSNP
rs754791169 362 dbSNP
rs773751153 366 dbSNP
rs772549621 368 dbSNP
rs748524758 371 dbSNP
rs779337491 378 dbSNP
rs755236452 380 dbSNP
rs777338465 381 dbSNP
rs1169610410 384 dbSNP
rs1476970349 388 dbSNP
rs749544825 395 dbSNP
rs1199789826 400 dbSNP
rs780383258 405 dbSNP
rs1265307954 406 dbSNP
rs940315351 406 dbSNP
rs1249233766 413 dbSNP
rs756301736 415 dbSNP
rs750507609 418 dbSNP
rs1274443629 421 dbSNP
rs767621764 422 dbSNP
rs757216968 426 dbSNP
rs1441436106 430 dbSNP
rs1324107494 433 dbSNP
rs1275959039 436 dbSNP
rs1048300592 437 dbSNP
rs1225796352 438 dbSNP
rs34973347 441 dbSNP
rs905017022 442 dbSNP
rs148903585 451 dbSNP
rs1410624417 452 dbSNP
rs1159801427 464 dbSNP
rs1421499710 474 dbSNP
rs762610409 477 dbSNP
rs370387187 479 dbSNP
rs1412688845 483 dbSNP
rs949152383 483 dbSNP
rs1401489757 485 dbSNP
rs1177045853 487 dbSNP
rs1176467345 488 dbSNP
rs1446444964 490 dbSNP
rs1481320309 491 dbSNP
rs1409443443 492 dbSNP
rs866924336 499 dbSNP
rs764840485 500 dbSNP
rs377163612 502 dbSNP
rs1207495983 503 dbSNP
rs950180642 504 dbSNP
rs568106095 505 dbSNP
rs770359441 511 dbSNP
rs188613442 518 dbSNP
rs774668767 529 dbSNP
rs1267842600 530 dbSNP
rs769094628 531 dbSNP
rs936298638 533 dbSNP
rs1375710701 536 dbSNP
rs1205803341 538 dbSNP
rs548382504 544 dbSNP
rs1447463338 546 dbSNP
rs570689044 551 dbSNP
rs1341836433 552 dbSNP
rs770126261 554 dbSNP
rs1353145198 556 dbSNP
rs746012169 557 dbSNP
rs781425989 561 dbSNP
rs757228094 564 dbSNP
rs751539437 566 dbSNP
rs777534286 569 dbSNP
rs758256074 571 dbSNP
rs1179726772 572 dbSNP
rs1206352237 576 dbSNP
rs1472200617 576 dbSNP
rs1243174793 577 dbSNP
rs752471855 579 dbSNP
rs1463885556 581 dbSNP
rs1247799132 584 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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' acccugagguacgggGUUc 5'
                         ||| 
Target 5' ---------------CAAa 3'
1 - 4
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 GSM1084064
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noemetine_AbnovaAb
Location of target site ENST00000396420.3 | 3UTR | caaaggaggagggagc
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 GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000396420.3 | 3UTR | caaaggaggagggagc
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
66 hsa-miR-4260 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT074404 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT289774 PER1 period circadian clock 1 2 2
MIRT442576 HOXD9 homeobox D9 2 2
MIRT443878 CNKSR3 CNKSR family member 3 2 2
MIRT449080 XPO6 exportin 6 2 2
MIRT450294 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT461785 FXR2 FMR1 autosomal homolog 2 2 2
MIRT463931 WNT10B Wnt family member 10B 2 2
MIRT464860 UBB ubiquitin B 2 8
MIRT467619 SLC7A5 solute carrier family 7 member 5 2 2
MIRT469649 RAC1 Rac family small GTPase 1 2 2
MIRT473421 MDM4 MDM4, p53 regulator 2 2
MIRT473646 MARCKSL1 MARCKS like 1 2 2
MIRT474213 LCOR ligand dependent nuclear receptor corepressor 2 2
MIRT474335 KMT2D lysine methyltransferase 2D 2 2
MIRT474871 KDELR1 KDEL endoplasmic reticulum protein retention receptor 1 2 2
MIRT477440 ELOVL5 ELOVL fatty acid elongase 5 2 2
MIRT478432 DAZAP2 DAZ associated protein 2 2 2
MIRT479851 CCDC6 coiled-coil domain containing 6 2 2
MIRT482507 ACTB actin beta 2 2
MIRT485473 IGF1R insulin like growth factor 1 receptor 2 8
MIRT485670 CCDC64 BICD family like cargo adaptor 1 2 4
MIRT485902 PGPEP1 pyroglutamyl-peptidase I 2 4
MIRT488143 PRRC2B proline rich coiled-coil 2B 2 4
MIRT489455 MSC musculin 2 2
MIRT509568 HIST2H2AB histone cluster 2 H2A family member b 2 4
MIRT513093 DYNAP dynactin associated protein 2 2
MIRT513256 CALM3 calmodulin 3 2 2
MIRT514356 UBBP4 ubiquitin B pseudogene 4 2 6
MIRT522019 PAQR3 progestin and adipoQ receptor family member 3 2 4
MIRT523164 HIST3H3 histone cluster 3 H3 2 2
MIRT523297 HIST1H1B histone cluster 1 H1 family member b 2 2
MIRT524782 BAG5 BCL2 associated athanogene 5 2 2
MIRT530921 SCIN scinderin 2 2
MIRT533302 USP44 ubiquitin specific peptidase 44 2 2
MIRT552782 YIPF4 Yip1 domain family member 4 2 4
MIRT553981 SRPR SRP receptor alpha subunit 2 2
MIRT563126 ZNF215 zinc finger protein 215 2 2
MIRT569025 IL21R interleukin 21 receptor 2 2
MIRT573413 RPL18A ribosomal protein L18a 2 2
MIRT574877 Dnajc6 DnaJ heat shock protein family (Hsp40) member C6 2 3
MIRT607538 GLI2 GLI family zinc finger 2 2 2
MIRT607682 MAPK10 mitogen-activated protein kinase 10 2 3
MIRT623791 GK5 glycerol kinase 5 (putative) 2 2
MIRT628834 FAM151B family with sequence similarity 151 member B 2 2
MIRT635547 LEPREL1 prolyl 3-hydroxylase 2 2 2
MIRT635698 NMNAT2 nicotinamide nucleotide adenylyltransferase 2 2 2
MIRT635906 ARPC1B actin related protein 2/3 complex subunit 1B 2 2
MIRT649985 MSI1 musashi RNA binding protein 1 2 2
MIRT654900 POMGNT1 protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) 2 2
MIRT655116 PHF7 PHD finger protein 7 2 2
MIRT658958 DNAJC6 DnaJ heat shock protein family (Hsp40) member C6 2 3
MIRT659665 CDC42EP4 CDC42 effector protein 4 2 2
MIRT668946 CNBP CCHC-type zinc finger nucleic acid binding protein 2 2
MIRT691164 APOL6 apolipoprotein L6 2 2
MIRT692696 MEAF6 MYST/Esa1 associated factor 6 2 2
MIRT693245 HBS1L HBS1 like translational GTPase 2 2
MIRT695203 SCAMP3 secretory carrier membrane protein 3 2 2
MIRT701957 MINK1 misshapen like kinase 1 2 2
MIRT706802 APOL4 apolipoprotein L4 2 2
MIRT716899 CACNB2 calcium voltage-gated channel auxiliary subunit beta 2 2 2
MIRT717632 HLX H2.0 like homeobox 2 2
MIRT719052 ZNF281 zinc finger protein 281 2 2
MIRT722973 GDE1 glycerophosphodiester phosphodiesterase 1 2 2
MIRT723643 RPTN repetin 2 2
MIRT734708 NR3C2 nuclear receptor subfamily 3 group C member 2 4 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4260 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4260 Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-4260 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4260 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-4260 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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