miRTarBase - #MIRT082398


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pre-miRNA Information
pre-miRNA hsa-mir-4471   
Genomic Coordinates chr8: 100382763 - 100382845
Description Homo sapiens miR-4471 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4471
Sequence 49| UGGGAACUUAGUAGAGGUUUAA |70
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol HNRNPUL1   
Synonyms E1B-AP5, E1BAP5, HNRPUL1
Description heterogeneous nuclear ribonucleoprotein U like 1
Transcript NM_007040   
Other Transcripts NM_144732   
Expression
Putative miRNA Targets on HNRNPUL1
3'UTR of HNRNPUL1
(miRNA target sites are highlighted)		 
>HNRNPUL1|NM_007040|3'UTR
   1 CCAGTGTGACCCAGAGGCTCCCGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCTGCCTCGGCCCCTCCTCTGCCCCCGC
  81 CAGATCCCGTGGTGCTGGGGATGGGGTCATCCCAGGGCTGCCTCCCTCCAGCCCACTGCCTCCCCTCTGAGGGGCTTCCT
 161 TCCCCTCCATAGGGCCAGGCATTTTTTTCTGGATTCAAACAGGCAACAATGACCTTTTATTTTCTGTTTGTCCCCACCTC
 241 CCCAGCCTTCCACCTCCTGTTCTTCCTACCTTCTTCCTTTTTGACTAAATAATCCCCACCTCCCTTGATCATACAGTGAG
 321 GCTACAGTGACTGAGGGGAGAATCCCCTCCTGTTCACTCTCCCAACCCTGCTCCAGCCCCTCAGCTTCCCAGACCCTCAT
 401 GCAGTTGGTTGTAAATTCTCCCAGGAGCTGTTTTACTGTCTACTTTTCAGGATTAAAAAAAAAATCAAAACTTAAAAAAA
 481 AAAAAGTTTAAAAAGCAAAATGGGGAGGGGGAGGAAGCAGTGACTTTTTTTTGGTAATTATGCGCTTTTTTTTAATTTTT
 561 AGAATTTGTCTTTTTACTGTGGGTGGGCTGTTGATATTTCATCAAGATAAGCATTTCTTTCCTGAGTTCAGGTGACTGAG
 641 GAAGAGCCACAAAACAAAACACAACAAAACCAAACCACAGAATCATCTTTAACCCAACTTTTTATACGATGCCCCAGTTC
 721 CCCATAACTTTGCACACAAGCTTCTGTGTTCAGTTGAATTGTAACTGCTTTTTGTATTTGGAGAGAGTGACTATTGAACT
 801 TGAAACCTTTTATTCCGGGCGTCTTGGTAGTTTCTGGTGGGATTCAGTGGGTGAGAGGGAAGAAGGGGAGGTTGGGGGGC
 881 TCCTTCCCTTCAGAACTTGAAGTTTCTCCCACTGCCTCCTCTCCAGTGGTCTCCCAGGTGCCAGACCCAAAAGCTTTTCC
 961 TACAGTGATACCCTTTATTTTTACTTCCCCTTGACTCATATGTTTTAACATGATTTTAACAAACTGCACTTATTAAGAAA
1041 TGTGTTTGCCCTGTTTTGTTTGGTTTCGTTTTGTTTTCTTTGAATAAATGACATGGCACCTCCTAGCAGGAAGGAAGCAG
1121 GGTTGAAACCCTGAAGTGTTACTGCAGTTGGCCGTTAATTGGGGTGGGGGCCTCTTTAAAGGGAAATTATTTACTCATTC
1201 ATTAAACAACTTAACTGAAAAAAAAAAAAAAAAAA
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' aauUUGGAG---AUGAU------UCAAGGGu 5'
             |||:|:   ||| |      ||||||| 
Target 5' cccAACTTTTTATACGATGCCCCAGTTCCCc 3'
 693 - 723 149.00 -10.50
2 
miRNA  3' aauUUGGAGAU--GAUUCAAGGGu 5'
             | |||:||  :| | ||||| 
Target 5' gatACCCTTTATTTTTACTTCCCc 3'
 967 - 990 129.00 -12.00
3 
miRNA  3' aaUUUG----GAGAUGAUUCAAGggu 5'
            ||:|    ||:| ||:|||||   
Target 5' atAAGCATTTCTTTCCTGAGTTCagg 3'
 607 - 632 126.00 -12.62
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM6346646 1 COSMIC
COSN30156402 9 COSMIC
COSN31538312 23 COSMIC
COSN30515812 25 COSMIC
COSN30685004 40 COSMIC
COSN26979151 79 COSMIC
COSN30183542 89 COSMIC
COSN30174432 90 COSMIC
COSN30525059 95 COSMIC
COSN8260583 190 COSMIC
COSN6144469 255 COSMIC
COSN26573494 381 COSMIC
COSN31541045 397 COSMIC
COSN30543416 467 COSMIC
COSN20115830 486 COSMIC
COSN515666 544 COSMIC
COSN22541992 572 COSMIC
COSN31516396 703 COSMIC
COSN31542903 708 COSMIC
COSN31481933 745 COSMIC
COSN17566706 793 COSMIC
COSN31490906 797 COSMIC
COSN31576206 858 COSMIC
COSN8260584 896 COSMIC
COSN30542261 968 COSMIC
COSN31487223 1013 COSMIC
COSN31579883 1025 COSMIC
rs15052 906 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs752558817 1 dbSNP
rs1395331572 3 dbSNP
rs778289524 3 dbSNP
rs1264060707 5 dbSNP
rs748057397 5 dbSNP
rs756101880 6 dbSNP
rs777393717 8 dbSNP
rs1196909223 10 dbSNP
rs749115347 11 dbSNP
rs1360193684 14 dbSNP
rs771921721 14 dbSNP
rs771221645 23 dbSNP
rs1240255459 24 dbSNP
rs201085940 24 dbSNP
rs1365432232 29 dbSNP
rs746159786 33 dbSNP
rs371063909 34 dbSNP
rs775660344 36 dbSNP
rs200198044 37 dbSNP
rs753129898 47 dbSNP
rs1395176661 50 dbSNP
rs776800172 52 dbSNP
rs548910950 53 dbSNP
rs1263503201 57 dbSNP
rs551340411 61 dbSNP
rs927738774 70 dbSNP
rs939065857 76 dbSNP
rs1297619498 77 dbSNP
rs1212892724 78 dbSNP
rs570318656 79 dbSNP
rs930860820 80 dbSNP
rs530952219 84 dbSNP
rs1363921625 89 dbSNP
rs916227916 90 dbSNP
rs1008681792 105 dbSNP
rs1040513589 106 dbSNP
rs946641237 112 dbSNP
rs900188903 119 dbSNP
rs1199478127 130 dbSNP
rs1481235165 138 dbSNP
rs1043654431 139 dbSNP
rs1209079140 142 dbSNP
rs552571378 144 dbSNP
rs570809941 156 dbSNP
rs902385049 160 dbSNP
rs995856247 166 dbSNP
rs999366927 169 dbSNP
rs570005756 171 dbSNP
rs1317399507 180 dbSNP
rs1010154924 182 dbSNP
rs1225396663 190 dbSNP
rs901939097 198 dbSNP
rs749871285 208 dbSNP
rs1296260457 210 dbSNP
rs1392350815 211 dbSNP
rs1375901254 212 dbSNP
rs996641080 214 dbSNP
rs1465602378 218 dbSNP
rs1407435377 227 dbSNP
rs868438543 231 dbSNP
rs1470661086 232 dbSNP
rs534834752 242 dbSNP
rs1197635737 247 dbSNP
rs982243718 248 dbSNP
rs1252344364 252 dbSNP
rs1196224152 257 dbSNP
rs1457293953 258 dbSNP
rs928058725 276 dbSNP
rs959454954 284 dbSNP
rs990787351 298 dbSNP
rs1255635742 305 dbSNP
rs1028972907 314 dbSNP
rs1318931846 321 dbSNP
rs1307577544 322 dbSNP
rs750415400 333 dbSNP
rs1457987259 336 dbSNP
rs1339199330 349 dbSNP
rs1399383502 350 dbSNP
rs1179615090 358 dbSNP
rs1171661445 359 dbSNP
rs553423056 366 dbSNP
rs552284376 373 dbSNP
rs1365151130 374 dbSNP
rs147743230 381 dbSNP
rs1015128616 383 dbSNP
rs1156686825 384 dbSNP
rs962567772 389 dbSNP
rs1243692340 404 dbSNP
rs1047958420 414 dbSNP
rs1477255015 416 dbSNP
rs908063036 422 dbSNP
rs1174785166 423 dbSNP
rs944851340 434 dbSNP
rs1465120433 442 dbSNP
rs1353189342 451 dbSNP
rs1360530340 455 dbSNP
rs200936072 455 dbSNP
rs544291183 468 dbSNP
rs556858072 472 dbSNP
rs1332975602 474 dbSNP
rs900258268 474 dbSNP
rs995887223 474 dbSNP
rs981643424 481 dbSNP
rs1054162469 484 dbSNP
rs1386761423 501 dbSNP
rs1295903517 503 dbSNP
rs537166216 520 dbSNP
rs1402727325 521 dbSNP
rs1165423970 525 dbSNP
rs1385593668 525 dbSNP
rs892801198 525 dbSNP
rs1447848151 534 dbSNP
rs10826 544 dbSNP
rs960507255 545 dbSNP
rs1020604658 546 dbSNP
rs1448748720 546 dbSNP
rs990552603 556 dbSNP
rs1216112121 571 dbSNP
rs1490621809 583 dbSNP
rs1294466351 604 dbSNP
rs1208399052 612 dbSNP
rs574551589 629 dbSNP
rs1271274191 639 dbSNP
rs1317281911 643 dbSNP
rs535644164 653 dbSNP
rs1341764642 663 dbSNP
rs1216247959 664 dbSNP
rs1275949754 671 dbSNP
rs539330044 672 dbSNP
rs1365791447 681 dbSNP
rs1318136060 688 dbSNP
rs1325353556 694 dbSNP
rs765301336 697 dbSNP
rs923860532 705 dbSNP
rs935215749 708 dbSNP
rs1168357263 709 dbSNP
rs1034151262 716 dbSNP
rs959720772 729 dbSNP
rs1193001749 741 dbSNP
rs554152357 747 dbSNP
rs901653401 754 dbSNP
rs1271302346 758 dbSNP
rs1197278451 765 dbSNP
rs1450162055 771 dbSNP
rs1451325820 781 dbSNP
rs932112435 790 dbSNP
rs1201486317 792 dbSNP
rs1198020026 794 dbSNP
rs745495791 794 dbSNP
rs887819652 795 dbSNP
rs1319420872 802 dbSNP
rs1255646877 817 dbSNP
rs185960356 818 dbSNP
rs1217456253 821 dbSNP
rs1247791531 822 dbSNP
rs990859393 829 dbSNP
rs1027645895 831 dbSNP
rs752711315 848 dbSNP
rs1330249654 852 dbSNP
rs1014844088 858 dbSNP
rs1467159180 864 dbSNP
rs898091842 868 dbSNP
rs908138206 873 dbSNP
rs557494702 874 dbSNP
rs1035887915 880 dbSNP
rs959115425 898 dbSNP
rs1189633468 899 dbSNP
rs990606573 900 dbSNP
rs572790772 903 dbSNP
rs15052 906 dbSNP
rs1233769885 907 dbSNP
rs1162849640 919 dbSNP
rs879683320 930 dbSNP
rs1388863653 935 dbSNP
rs1456859231 947 dbSNP
rs1406863519 952 dbSNP
rs931755015 954 dbSNP
rs1339718010 955 dbSNP
rs1197467827 960 dbSNP
rs1233112575 963 dbSNP
rs777817960 966 dbSNP
rs1054194859 969 dbSNP
rs1280326766 972 dbSNP
rs1217078996 983 dbSNP
rs1343815668 988 dbSNP
rs751772978 989 dbSNP
rs566141783 1002 dbSNP
rs1330514719 1010 dbSNP
rs1280039333 1011 dbSNP
rs1340550012 1021 dbSNP
rs1360915612 1027 dbSNP
rs1312151412 1028 dbSNP
rs892833790 1030 dbSNP
rs945714178 1030 dbSNP
rs923579958 1034 dbSNP
rs935286451 1050 dbSNP
rs779846476 1055 dbSNP
rs976389995 1068 dbSNP
rs561785445 1069 dbSNP
rs545840022 1070 dbSNP
rs907121361 1095 dbSNP
rs923162893 1098 dbSNP
rs931815220 1102 dbSNP
rs757609624 1103 dbSNP
rs1441547620 1105 dbSNP
rs781682119 1111 dbSNP
rs141067767 1122 dbSNP
rs1266015454 1125 dbSNP
rs1351159641 1125 dbSNP
rs1478151098 1131 dbSNP
rs1308471712 1137 dbSNP
rs1246569554 1152 dbSNP
rs542415744 1154 dbSNP
rs746446199 1155 dbSNP
rs1447365579 1166 dbSNP
rs748770390 1166 dbSNP
rs1346020431 1168 dbSNP
rs771432362 1185 dbSNP
rs756624307 1195 dbSNP
rs1473919581 1197 dbSNP
rs1036342060 1202 dbSNP
rs894302397 1204 dbSNP
rs11671070 1207 dbSNP
rs563988590 1209 dbSNP
rs1164575537 1218 dbSNP
rs1003156914 1221 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 11100.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 "PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 11100.0
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 GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aauuUGGAGAU--GAUUCAAGGGu 5'
              |:||:||  | || ||::: 
Target 5' aaucAUCUUUAACCCAACUUUUUa 3'
 		1 - 24
Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000352456.3 | 3UTR | AAUCAUCUUUAACCCAACUUUUUAUACGAUGCCCCAGUUCCCCAUAACUUUGCACACAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000352456.3 | 3UTR | UUCCCCAUAACUUUGCACACAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1065668
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_7
Location of target site ENST00000352456.3 | 3UTR | UCCCCAUAACUUUGCACACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000352456.3 | 3UTR | AAUCAUCUUUAACCCAACUUUUUAUACGAUGCCCCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
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
51 hsa-miR-4471 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT082398 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 4
MIRT295740 KIF3B kinesin family member 3B 2 2
MIRT453005 CCDC115 coiled-coil domain containing 115 2 16
MIRT456180 ZDHHC6 zinc finger DHHC-type containing 6 2 2
MIRT457455 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT464992 TUBB2A tubulin beta 2A class IIa 2 10
MIRT467615 SLC7A5 solute carrier family 7 member 5 2 2
MIRT468602 SERBP1 SERPINE1 mRNA binding protein 1 2 2
MIRT470070 PTGES2 prostaglandin E synthase 2 2 2
MIRT470562 POU2F1 POU class 2 homeobox 1 2 2
MIRT472274 NFIB nuclear factor I B 2 2
MIRT473471 MCFD2 multiple coagulation factor deficiency 2 2 2
MIRT477892 DVL3 dishevelled segment polarity protein 3 2 4
MIRT486345 TACC2 transforming acidic coiled-coil containing protein 2 2 6
MIRT487190 NFASC neurofascin 2 4
MIRT488690 NAT9 N-acetyltransferase 9 (putative) 2 2
MIRT492106 TAB2 TGF-beta activated kinase 1/MAP3K7 binding protein 2 2 2
MIRT495216 DSCR3 DSCR3 arrestin fold containing 2 2
MIRT495666 TUBAL3 tubulin alpha like 3 2 2
MIRT501833 NCOA2 nuclear receptor coactivator 2 2 2
MIRT507147 GATAD2B GATA zinc finger domain containing 2B 2 4
MIRT508522 GDI1 GDP dissociation inhibitor 1 2 2
MIRT513839 KCTD15 potassium channel tetramerization domain containing 15 2 4
MIRT513883 GTF2IRD2 GTF2I repeat domain containing 2 2 4
MIRT527336 COL18A1 collagen type XVIII alpha 1 chain 2 2
MIRT537390 FGD6 FYVE, RhoGEF and PH domain containing 6 2 2
MIRT538879 BTBD1 BTB domain containing 1 2 2
MIRT539044 ATXN1L ataxin 1 like 2 4
MIRT554387 SERTAD3 SERTA domain containing 3 2 2
MIRT554936 RAP1A RAP1A, member of RAS oncogene family 2 2
MIRT567517 FOXC1 forkhead box C1 2 2
MIRT573598 CERS1 ceramide synthase 1 2 2
MIRT642417 CILP2 cartilage intermediate layer protein 2 2 2
MIRT643296 PHKG1 phosphorylase kinase catalytic subunit gamma 1 2 2
MIRT652883 SYVN1 synoviolin 1 2 2
MIRT657928 GATSL2 cytosolic arginine sensor for mTORC1 subunit 2 2 2
MIRT660302 BHLHE40 basic helix-loop-helix family member e40 2 2
MIRT664717 SLC7A6OS solute carrier family 7 member 6 opposite strand 2 2
MIRT698889 SPTBN2 spectrin beta, non-erythrocytic 2 2 2
MIRT702007 MIDN midnolin 2 2
MIRT706808 APOL4 apolipoprotein L4 2 2
MIRT708330 DERL2 derlin 2 2 2
MIRT709885 ERCC6L ERCC excision repair 6 like, spindle assembly checkpoint helicase 2 2
MIRT711887 INSIG2 insulin induced gene 2 2 2
MIRT711956 CYP27B1 cytochrome P450 family 27 subfamily B member 1 2 2
MIRT715081 PRKAB2 protein kinase AMP-activated non-catalytic subunit beta 2 2 2
MIRT716218 TRIM17 tripartite motif containing 17 2 2
MIRT718124 CHST4 carbohydrate sulfotransferase 4 2 2
MIRT718725 VWA9 integrator complex subunit 14 2 2
MIRT719450 APBA1 amyloid beta precursor protein binding family A member 1 2 2
MIRT725666 ABI2 abl interactor 2 2 2
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-4471 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-4471 Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-miR-4471 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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