miRTarBase - #MIRT450883


—
pre-miRNA Information
pre-miRNA hsa-mir-3171   
Genomic Coordinates chr14: 27633205 - 27633278
Description Homo sapiens miR-3171 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3171
Sequence 10| AGAUGUAUGGAAUCUGUAUAUAUC |33
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1317334268 4 dbSNP
rs1412633952 16 dbSNP
rs967845497 17 dbSNP
rs1278913737 19 dbSNP
rs1348410638 24 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol COL4A5   
Synonyms ASLN, ATS, CA54
Description collagen type IV alpha 5 chain
Transcript NM_000495   
Other Transcripts NM_033380   
Expression
Putative miRNA Targets on COL4A5
3'UTR of COL4A5
(miRNA target sites are highlighted)		 
>COL4A5|NM_000495|3'UTR
   1 CATTTTGAAGAATTCCTTTTGTGTTTTAAAATGTGATATATATATATATAAAATTCCTAGGATGCAGTGTCTCATTGTCC
  81 CCAACTTTACTACTGCTGCCGTCAATGGTGCTACTATATATGATCAAGATAACATGCTGACTAGTAACCATGAAGATTCA
 161 GATGTACCTCAGCAATGCGCCAGAGCAAAGTCTCTATTATTTTTCTACTAAAGAAATAAGGAAGTGAATTTACTTTTTGG
 241 GTCCAGAATGACTTTCTCCAAGAATTATAAGATGAAAATTATATATTTTGCCCAGTTACTAAAATGGTACATTAAAAATT
 321 CAATTAAGAGAAGAGTCACATTGAGTAAAATAAAAGACTGCAGTTTGTGGGAAGAATTATTTTTCACGGTGCTACTAATC
 401 CTGCTGTATCCCGGGTTTTTAATATAAAGGTGTTAAGCTTATTTTGCTTTGTAAGTAAAGAATGTGTATATTGTGAACAG
 481 CCTTTTAGCTCAAAATGTTGAGTCATTTACATATGACATAGCATGAATCACTCTTTACAGAAAATGTAGGAAACCCTAGA
 561 ATACAGACAGCAATATTTTATATTCATGTTTATCAAAGTGAGAGGACTTATATTCCTACATCAAGTTACTACTGAGAGTA
 641 AATTTATTTTGAGTTTTATCCCGTAAGTTCTGTTTTGATTTTTTTTAAAAAACAAACCCTTTTAGTCACTTTAATCAGAA
 721 TTTTAAATGTTCATGTTACATACCAAATTATAATATCTAATGGAGCAATTTGTCTTTTGCTATATTCTCCAAGATTATCT
 801 CTTAAGACCATATGCCCCCTGTTTTAATGTTTCTTACATCTTGTTTTTACTCATTTCTGACTGGACAAAGTTCTTCCAAA
 881 CAATTCTGAGAAACAAAAACACACACGCAGAATTAACAATTCTTTTCCCTGTGCTTCTTATGTAAGAATCCTCCTGTGGC
 961 CTCTGCTTGTACAGAACTGGGAAACAACACTTGGTTAGTCTCTTTTAAGTTACAAAAAGCCAATTGATGTTTCTTATTCT
1041 TTTTAAATTTTAAATATTTTGTTATAAATACTCACAGGATACCTTATTTCCCTAGCTATCATCTCCTGACTTAATGTTTT
1121 TTAAACCCACCAATATAAATTTAATTAAAGATATATGTTGTAAGGATAAAAAAAAAAAAAAAA
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' cuAUAUAUGUCUAAGGUAUGUAGa 5'
            |:| |  | :||:| |||||| 
Target 5' ccTGTTTTAATGTTTCTTACATCt 3'
 818 - 841 134.00 -9.20
2 
miRNA  3' cuAUA---UAUGUCUAAGGUAUGUAGa 5'
            |||   ||: | |||  |||:||: 
Target 5' atTATAAGATGAAAATT--ATATATTt 3'
 264 - 288 126.00 -6.20
3 
miRNA  3' cuauauaUGUCUA-AGGUAUGUAGa 5'
                 ||  || |:| |||||| 
Target 5' tgagaggACTTATATTCCTACATCa 3'
 599 - 623 125.00 -9.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
24793 49 ClinVar
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1020440109 2 dbSNP
rs774707459 12 dbSNP
rs1335210452 26 dbSNP
rs1443079075 30 dbSNP
rs1248825655 36 dbSNP
rs753965990 36 dbSNP
rs754794392 36 dbSNP
rs761103848 36 dbSNP
rs762112047 42 dbSNP
rs768015387 45 dbSNP
rs959589081 49 dbSNP
rs1262210475 50 dbSNP
rs750945137 52 dbSNP
rs1296866253 54 dbSNP
rs985771638 63 dbSNP
rs1382803618 83 dbSNP
rs1305190810 91 dbSNP
rs1229179113 101 dbSNP
rs920686487 102 dbSNP
rs951987726 106 dbSNP
rs1471667836 117 dbSNP
rs1374746266 121 dbSNP
rs1193739294 131 dbSNP
rs1260404904 139 dbSNP
rs1292485778 162 dbSNP
rs983449432 163 dbSNP
rs763169312 171 dbSNP
rs1208462476 174 dbSNP
rs1221521254 179 dbSNP
rs143875350 180 dbSNP
rs781246031 192 dbSNP
rs1227251625 197 dbSNP
rs1040992491 208 dbSNP
rs1195290988 210 dbSNP
rs1285250736 219 dbSNP
rs1260591436 224 dbSNP
rs1345153975 225 dbSNP
rs1474882326 233 dbSNP
rs1321778405 234 dbSNP
rs922406361 235 dbSNP
rs1182179853 238 dbSNP
rs1415727679 245 dbSNP
rs1421876046 247 dbSNP
rs932516268 256 dbSNP
rs540226075 261 dbSNP
rs565614113 268 dbSNP
rs1043804690 270 dbSNP
rs1461410885 284 dbSNP
rs1420900859 291 dbSNP
rs1200919734 298 dbSNP
rs1480455327 304 dbSNP
rs893558588 310 dbSNP
rs946506160 311 dbSNP
rs1196232508 317 dbSNP
rs371346512 322 dbSNP
rs1002179205 323 dbSNP
rs767680837 324 dbSNP
rs1274142271 332 dbSNP
rs1195781696 334 dbSNP
rs1055019004 362 dbSNP
rs894403555 365 dbSNP
rs376179598 367 dbSNP
rs1361153768 380 dbSNP
rs1014084464 388 dbSNP
rs753003990 389 dbSNP
rs1444633482 395 dbSNP
rs1035296086 407 dbSNP
rs756432328 413 dbSNP
rs1329270707 414 dbSNP
rs1446001255 416 dbSNP
rs777812281 425 dbSNP
rs1178441153 431 dbSNP
rs1469876946 432 dbSNP
rs1012421275 437 dbSNP
rs753683903 438 dbSNP
rs746003559 448 dbSNP
rs769873385 480 dbSNP
rs1170513395 501 dbSNP
rs756687457 513 dbSNP
rs1286280357 518 dbSNP
rs952101309 525 dbSNP
rs369440184 526 dbSNP
rs756937785 534 dbSNP
rs983564131 551 dbSNP
rs1233861158 569 dbSNP
rs1245765321 584 dbSNP
rs1181584202 587 dbSNP
rs1456683717 605 dbSNP
rs1014917262 608 dbSNP
rs1245531870 611 dbSNP
rs1204793358 618 dbSNP
rs1460982074 621 dbSNP
rs1276575714 631 dbSNP
rs1310618670 643 dbSNP
rs1356552977 654 dbSNP
rs1351633155 664 dbSNP
rs966092524 665 dbSNP
rs977048497 678 dbSNP
rs1218088029 679 dbSNP
rs922550729 680 dbSNP
rs778978745 687 dbSNP
rs932436136 687 dbSNP
rs985255608 688 dbSNP
rs1453278154 692 dbSNP
rs1358128064 694 dbSNP
rs915107851 696 dbSNP
rs1446020630 699 dbSNP
rs1331589407 701 dbSNP
rs1210343207 703 dbSNP
rs1401901693 709 dbSNP
rs946455544 733 dbSNP
rs1157619414 734 dbSNP
rs1238890409 735 dbSNP
rs1042143518 740 dbSNP
rs902152302 741 dbSNP
rs939043127 742 dbSNP
rs1057079819 764 dbSNP
rs1182827685 769 dbSNP
rs1380762378 773 dbSNP
rs1235843892 774 dbSNP
rs1218076386 775 dbSNP
rs1447604751 788 dbSNP
rs1283842152 790 dbSNP
rs56366649 797 dbSNP
rs1351314890 810 dbSNP
rs1316872141 817 dbSNP
rs1246682976 829 dbSNP
rs1378393621 830 dbSNP
rs1282311472 837 dbSNP
rs1432308542 838 dbSNP
rs186307993 844 dbSNP
rs1012538268 866 dbSNP
rs1027812466 872 dbSNP
rs1377271576 901 dbSNP
rs1417469551 904 dbSNP
rs771621007 905 dbSNP
rs1164575572 907 dbSNP
rs1423557430 918 dbSNP
rs1407391804 920 dbSNP
rs1412289368 923 dbSNP
rs779508941 923 dbSNP
rs1188740543 934 dbSNP
rs910180762 937 dbSNP
rs746484022 943 dbSNP
rs768368622 952 dbSNP
rs1004950231 967 dbSNP
rs1336378365 979 dbSNP
rs976324765 986 dbSNP
rs1191847874 989 dbSNP
rs1490895155 996 dbSNP
rs1292729319 999 dbSNP
rs914084019 1004 dbSNP
rs1320830748 1009 dbSNP
rs191043562 1012 dbSNP
rs1216257041 1022 dbSNP
rs1015031535 1026 dbSNP
rs182458116 1028 dbSNP
rs763266472 1030 dbSNP
rs1347039910 1041 dbSNP
rs1452369530 1044 dbSNP
rs199836099 1047 dbSNP
rs1044259626 1059 dbSNP
rs1348428016 1065 dbSNP
rs1029446064 1078 dbSNP
rs1379690948 1079 dbSNP
rs1423068344 1087 dbSNP
rs1238644154 1092 dbSNP
rs953977378 1096 dbSNP
rs771711362 1097 dbSNP
rs1349301766 1098 dbSNP
rs1190761191 1106 dbSNP
rs1488074064 1108 dbSNP
rs1244756096 1115 dbSNP
rs188323700 1127 dbSNP
rs1206604102 1131 dbSNP
rs375602334 1135 dbSNP
rs1219362266 1145 dbSNP
rs1280288276 1148 dbSNP
rs915057091 1152 dbSNP
rs1014158032 1155 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions BC-1
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 GSM796037. RNA binding protein: AGO2. Condition:4-Thiouridine ...

- Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' cuauauaugucuaagguAUGuaga 5'
                           |||    
Target 5' -----------ucaaguUACuacu 3'
 		1 - 13
Article - Gottwein E; Corcoran DL; Mukherjee N; et al.
- Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
CLIP-seq Support 1 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_033380 | 3UTR | GUUUAUCAAAGUGAGAGGACUUAUAUUCCUACAUCAAGUUACUACUGAGAGUAAAUUUAUUUUGAGUUUUAUCCCGUAAGUUCUGUUUUGAUUUUUUUUAAAAAACAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903834
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_b
Location of target site NM_000495 | 3UTR | CAAAGUGAGAGGACUUAUAUUCCUACAUCAAGUUACUACUGAGAGUAAAUUUAUUUUGAGUUUUAUCCCGUAAGUUCUGUUUUGAUUUUUUUUAAAAAACAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_000495 | 3UTR | UUAUAUUCCUACAUCAAGUUACUACUGAGAGUAAAUUUAUUUUGAGUUUUAUCCCGUAAGUUCUGUUUUGAUUUUUUUUAAAAAACAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_000495 | 3UTR | GGACUUAUAUUCCUACAUCAAGUUACUACUGAGAGUAAAUUUAUUUUGAGUUUUAUCCCGUAAGUUCUGUUUUGAUUUUUUUUAAAAAACAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM796037
Method / RBP PAR-CLIP / AGO2
Cell line / Condition BC-1 / 4-Thiouridine
Location of target site ENST00000361603.2 | 3UTR | UCAAGUUACUACUGAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22100165 / GSE32109
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
Click to see details
37 hsa-miR-3171 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT117345 MAPRE2 microtubule associated protein RP/EB family member 2 2 2
MIRT152426 ARID3A AT-rich interaction domain 3A 2 2
MIRT227670 SET SET nuclear proto-oncogene 2 2
MIRT293606 PVR poliovirus receptor 2 2
MIRT442923 TFDP2 transcription factor Dp-2 2 2
MIRT447007 RSF1 remodeling and spacing factor 1 2 2
MIRT450195 ZHX3 zinc fingers and homeoboxes 3 2 2
MIRT450883 COL4A5 collagen type IV alpha 5 chain 2 2
MIRT459707 ZNF641 zinc finger protein 641 2 2
MIRT467111 SRI sorcin 2 2
MIRT468271 SFXN1 sideroflexin 1 2 2
MIRT484168 WDR82P1 WD repeat domain 82 pseudogene 1 2 8
MIRT502274 H3F3B H3 histone family member 3B 2 4
MIRT504190 FAM127B retrotransposon Gag like 8A 2 2
MIRT507718 CMPK1 cytidine/uridine monophosphate kinase 1 2 6
MIRT513852 JARID2 jumonji and AT-rich interaction domain containing 2 2 8
MIRT521900 PIAS1 protein inhibitor of activated STAT 1 2 2
MIRT525975 SPA17 sperm autoantigenic protein 17 2 2
MIRT534599 RORA RAR related orphan receptor A 2 2
MIRT537572 ESYT2 extended synaptotagmin 2 2 2
MIRT539261 ANKRD44 ankyrin repeat domain 44 2 2
MIRT544214 SRSF11 serine and arginine rich splicing factor 11 2 4
MIRT553877 SUPT7L SPT7 like, STAGA complex gamma subunit 2 4
MIRT564547 CCDC80 coiled-coil domain containing 80 2 2
MIRT571228 SYT9 synaptotagmin 9 2 2
MIRT572016 H3F3C H3 histone family member 3C 2 2
MIRT613116 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 2 2
MIRT629028 MMP16 matrix metallopeptidase 16 2 4
MIRT635228 CD59 CD59 molecule (CD59 blood group) 2 2
MIRT641493 POLA2 DNA polymerase alpha 2, accessory subunit 2 2
MIRT648008 ZNF431 zinc finger protein 431 2 2
MIRT697344 ZNF544 zinc finger protein 544 2 2
MIRT700991 PDE3A phosphodiesterase 3A 2 2
MIRT704714 CHD9 chromodomain helicase DNA binding protein 9 2 2
MIRT705320 ATP2A2 ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 2 2
MIRT705387 ATP1B3 ATPase Na+/K+ transporting subunit beta 3 2 2
MIRT715811 NUDT7 nudix hydrolase 7 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-3171 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)
hsa-miR-3171 Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-3171 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3171 Ceritinib 57379345 NSC776422 approved resistant cell line (H3122)

Error report submission