pre-miRNA Information
pre-miRNA hsa-mir-4491   
Genomic Coordinates chr11: 111347757 - 111347824
Description Homo sapiens miR-4491 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4491
Sequence 46| AAUGUGGACUGGUGUGACCAAA |67
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1043555759 4 dbSNP
rs1182248607 6 dbSNP
rs527936256 7 dbSNP
rs755554417 14 dbSNP
rs779628583 16 dbSNP
rs1471408223 19 dbSNP
rs909066815 20 dbSNP
Putative Targets

Gene Information
Gene Symbol RBM22   
Synonyms Cwc2, ZC3H16, fSAP47
Description RNA binding motif protein 22
Transcript NM_018047   
Expression
Putative miRNA Targets on RBM22
3'UTR of RBM22
(miRNA target sites are highlighted)
>RBM22|NM_018047|3'UTR
   1 CACCTTGTCACCACTCTGGGGCTCTGTGGAAGAAAGGGCACTTAAAACTCCCAGTAAATCTTGGAATAAATATATTTTTC
  81 CTTCCCTTGTAGTTTCCATGGTAGCTGAATGTGCTCAGATGTGAGCAGTCAGAGACTGACAGCCATGCTTTCCTATACTT
 161 GTTCAAAGGATCGATGGACCGTAAATAAGCTGCCATTAACACATCTGGTTACTGCTGTAACATGACTAATAAAACCGAAC
 241 GCCTGTTCCCCTTACCCGTGTGGGGGACACGCAGATGAGTGAATTGGAATGTCCAGCAGAGTTACCCTCCCAATTATATG
 321 TTCATTTTGTATATTTTTTGGTCGGGGGAAAAATTGACCTGCAGTAAAAAAACCTTTGACCATTTTTATGTCCATTGGAT
 401 ACTTTCCTTTTTATCATCTTAAAAAAAGATAACTAGTACTAATCATTGTAGTGGCCTAAGTGTGATTTAACTCTTGAAGT
 481 CACACCCTCCGAAAGATGAGTAGAAACCAGCACCAGCACAGCCCAGATCTTCTCTTTCCTCTCCTTTTCCTCATTTATTC
 561 CTAAAGGAATCTGACCATTTTACGTCTCTACGGCCCAAAAAAAGACAAAAATAAAAATTCCTTTTTATTCCTGTCAACTG
 641 GATGGAAACACAAATTTCATGGAGCTGTGTACCATCGAAGAAACCTGGTGTCTGGCATGAAATTACTGTAAAGAACTTCC
 721 TGTAAAACACGTTCTTTAACAAACTGAAATGAAAAGCATTGGAGCGTCTGAATGAAAGACGTGACCTCCTGCTGGGACTC
 801 TGATGGTCTTCAGCATTCACCTTCGTGTGTCTTCAGTGTCTCATTGTCATCCCTGCTTCTGTTTGGTCTTAGAGTGTTTG
 881 GATATAACTGAATTGTAGATGGTAAAGGAAATTTGATGTGTTTTTTGTTTTTAAATAATTAAAACGGGTCAATTTTTCAC
 961 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' aaaCCAGUGUGGUCAGGUGUaa 5'
             ||||| |::  |:||||  
Target 5' acgGGTCA-ATT-TTTCACAaa 3'
944 - 963 117.00 -11.00
2
miRNA  3' aaACCAG-UGUGGUCAGGUGUAa 5'
            |||||  || || |:||| | 
Target 5' gaTGGTCTTCAGCA-TTCACCTt 3'
802 - 823 115.00 -13.12
3
miRNA  3' aaaccAGUGUGGUCAGGUGUAa 5'
               ||  |||| |::||:| 
Target 5' aggaaTCTGACCATTTTACGTc 3'
565 - 586 113.00 -10.40
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30622842 21 COSMIC
COSN19671945 36 COSMIC
COSN510350 56 COSMIC
COSN16483540 61 COSMIC
COSN31573599 78 COSMIC
COSN30190267 108 COSMIC
COSN14149410 116 COSMIC
COSN31486443 123 COSMIC
COSN30452901 172 COSMIC
COSN31962498 258 COSMIC
COSN21872071 356 COSMIC
COSN9928682 439 COSMIC
COSN6867663 730 COSMIC
COSN31962497 780 COSMIC
COSN16536556 879 COSMIC
COSN28443383 896 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs892349842 3 dbSNP
rs760584334 4 dbSNP
rs1052277967 5 dbSNP
rs774334881 7 dbSNP
rs1296910844 9 dbSNP
rs766510502 12 dbSNP
rs762892672 14 dbSNP
rs1304911272 23 dbSNP
rs1176466859 29 dbSNP
rs773495291 31 dbSNP
rs912684635 37 dbSNP
rs376368982 38 dbSNP
rs770073028 39 dbSNP
rs1189919945 40 dbSNP
rs1415897325 41 dbSNP
rs748588315 48 dbSNP
rs765262663 48 dbSNP
rs932660096 64 dbSNP
rs1171396125 66 dbSNP
rs866768622 80 dbSNP
rs1375453106 82 dbSNP
rs546431416 89 dbSNP
rs964972116 93 dbSNP
rs1416614464 94 dbSNP
rs974451557 96 dbSNP
rs962999304 114 dbSNP
rs1172410872 115 dbSNP
rs1016220964 118 dbSNP
rs1166086179 133 dbSNP
rs1354367613 133 dbSNP
rs1218713769 140 dbSNP
rs1279527002 146 dbSNP
rs982951917 148 dbSNP
rs191874795 154 dbSNP
rs1305746010 155 dbSNP
rs1203697514 164 dbSNP
rs909399563 172 dbSNP
rs984969172 180 dbSNP
rs140724583 181 dbSNP
rs1194544920 191 dbSNP
rs1001891487 195 dbSNP
rs1180197318 196 dbSNP
rs1026402303 200 dbSNP
rs1170395822 202 dbSNP
rs1002923248 207 dbSNP
rs866279310 209 dbSNP
rs971835989 211 dbSNP
rs1022960904 212 dbSNP
rs1021976386 217 dbSNP
rs1258251564 227 dbSNP
rs1013281187 233 dbSNP
rs78294632 235 dbSNP
rs1032868767 236 dbSNP
rs1277807756 237 dbSNP
rs1224191237 240 dbSNP
rs188314076 241 dbSNP
rs151318348 244 dbSNP
rs890273642 256 dbSNP
rs369557607 257 dbSNP
rs183825665 258 dbSNP
rs1485493579 269 dbSNP
rs932763958 270 dbSNP
rs1265555012 271 dbSNP
rs11406 284 dbSNP
rs1185943637 296 dbSNP
rs1268672190 303 dbSNP
rs1304118392 304 dbSNP
rs191957973 309 dbSNP
rs1445140826 313 dbSNP
rs1357986528 317 dbSNP
rs1039357991 321 dbSNP
rs149187992 325 dbSNP
rs1414568637 331 dbSNP
rs1157244082 340 dbSNP
rs941356188 341 dbSNP
rs982984415 343 dbSNP
rs1293604578 347 dbSNP
rs1369716852 349 dbSNP
rs1438592691 358 dbSNP
rs909482513 363 dbSNP
rs147788860 365 dbSNP
rs1035171014 373 dbSNP
rs980879227 374 dbSNP
rs1183724249 380 dbSNP
rs540830756 381 dbSNP
rs773363277 382 dbSNP
rs1470252157 386 dbSNP
rs1022426165 388 dbSNP
rs878933522 390 dbSNP
rs373615599 393 dbSNP
rs1252867263 395 dbSNP
rs1236902060 405 dbSNP
rs929466526 406 dbSNP
rs573440741 407 dbSNP
rs1476386126 408 dbSNP
rs981971014 412 dbSNP
rs1010603198 413 dbSNP
rs1164917691 418 dbSNP
rs12187120 420 dbSNP
rs1466099140 424 dbSNP
rs892110765 428 dbSNP
rs763982175 429 dbSNP
rs1207842514 445 dbSNP
rs971495293 448 dbSNP
rs1023444823 458 dbSNP
rs1030945746 459 dbSNP
rs1448721749 471 dbSNP
rs991526379 486 dbSNP
rs957563627 490 dbSNP
rs745932971 491 dbSNP
rs1337067202 492 dbSNP
rs1211831078 504 dbSNP
rs998722372 507 dbSNP
rs781712539 513 dbSNP
rs757692363 517 dbSNP
rs1226184674 521 dbSNP
rs1458599786 523 dbSNP
rs1377720585 528 dbSNP
rs1284136067 530 dbSNP
rs554977452 532 dbSNP
rs903063630 537 dbSNP
rs566133637 540 dbSNP
rs998371807 542 dbSNP
rs996373430 546 dbSNP
rs1415451654 548 dbSNP
rs1473948656 549 dbSNP
rs1391324253 553 dbSNP
rs899953695 553 dbSNP
rs1163499156 560 dbSNP
rs899594530 562 dbSNP
rs748621314 563 dbSNP
rs1039836696 568 dbSNP
rs145285842 569 dbSNP
rs1326651621 571 dbSNP
rs888077570 572 dbSNP
rs1049374063 583 dbSNP
rs575113363 584 dbSNP
rs768878033 591 dbSNP
rs556954556 592 dbSNP
rs764923827 601 dbSNP
rs981648401 603 dbSNP
rs969960008 604 dbSNP
rs754596408 621 dbSNP
rs915023838 622 dbSNP
rs1189169059 636 dbSNP
rs1216805197 641 dbSNP
rs1271458911 644 dbSNP
rs916001469 647 dbSNP
rs989615030 648 dbSNP
rs1211193859 657 dbSNP
rs538339154 666 dbSNP
rs991950846 667 dbSNP
rs1484484109 676 dbSNP
rs957403073 677 dbSNP
rs1246089849 698 dbSNP
rs1476085931 699 dbSNP
rs1166107747 702 dbSNP
rs1418631193 704 dbSNP
rs1414827840 716 dbSNP
rs1335929743 722 dbSNP
rs1187759987 725 dbSNP
rs1030684471 730 dbSNP
rs1488681743 734 dbSNP
rs1413136773 741 dbSNP
rs925954722 746 dbSNP
rs1341249380 758 dbSNP
rs753396207 759 dbSNP
rs1268950465 765 dbSNP
rs967254562 766 dbSNP
rs1220244830 770 dbSNP
rs1282897853 772 dbSNP
rs1345358433 777 dbSNP
rs553986768 780 dbSNP
rs954612230 781 dbSNP
rs1448236080 784 dbSNP
rs749717913 788 dbSNP
rs766425991 798 dbSNP
rs1175331803 802 dbSNP
rs577391444 802 dbSNP
rs996058712 803 dbSNP
rs898980839 811 dbSNP
rs998047208 817 dbSNP
rs546343444 822 dbSNP
rs1038478751 824 dbSNP
rs534519615 825 dbSNP
rs567518103 834 dbSNP
rs779565997 835 dbSNP
rs1018030812 836 dbSNP
rs1233949376 837 dbSNP
rs1368666892 841 dbSNP
rs1286290981 848 dbSNP
rs1295519517 867 dbSNP
rs1456539718 874 dbSNP
rs1352385539 876 dbSNP
rs549029246 878 dbSNP
rs939318797 880 dbSNP
rs1005704685 881 dbSNP
rs530868716 884 dbSNP
rs928261165 897 dbSNP
rs1046745006 908 dbSNP
rs1251013245 921 dbSNP
rs1169358261 927 dbSNP
rs1453594202 933 dbSNP
rs1431691117 939 dbSNP
rs993807723 945 dbSNP
rs867241174 946 dbSNP
rs1045708867 947 dbSNP
rs1455530418 952 dbSNP
rs898100564 954 dbSNP
rs948267830 960 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 55696.0
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 ...

- 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 55696.0
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 GSM1065667. RNA binding protein: AGO1. 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' aaaccagUGUGGUCAGGUGUAa 5'
                 |||:|  ||||||| 
Target 5' -------ACAUC--UCCACAUa 3'
1 - 13
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 ENST00000199814.4 | 3UTR | AUACACAUACAUACAUACAUAUAUG
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 GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000199814.4 | 3UTR | ACAUCUCCACAUACACAUACAUACAUACAUAUAUG
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
67 hsa-miR-4491 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056779 ARID5B AT-rich interaction domain 5B 2 2
MIRT061577 BTG2 BTG anti-proliferation factor 2 2 2
MIRT063828 SRP9 signal recognition particle 9 2 4
MIRT102306 DNAJB9 DnaJ heat shock protein family (Hsp40) member B9 2 10
MIRT186634 COX20 COX20, cytochrome c oxidase assembly factor 2 8
MIRT191243 STYX serine/threonine/tyrosine interacting protein 2 2
MIRT195908 SRSF11 serine and arginine rich splicing factor 11 2 4
MIRT240343 UBXN2B UBX domain protein 2B 2 2
MIRT271178 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT286219 TMEM97 transmembrane protein 97 2 4
MIRT314182 OCLN occludin 2 4
MIRT323938 AKAP2 A-kinase anchoring protein 2 2 4
MIRT323940 PALM2-AKAP2 PALM2-AKAP2 readthrough 2 4
MIRT340113 TXLNA taxilin alpha 2 2
MIRT450333 LRWD1 leucine rich repeats and WD repeat domain containing 1 2 2
MIRT451283 ZNF101 zinc finger protein 101 2 2
MIRT451879 SOD2 superoxide dismutase 2 2 8
MIRT453577 CRCP CGRP receptor component 2 2
MIRT454366 ASAH2 N-acylsphingosine amidohydrolase 2 2 2
MIRT454797 STOML3 stomatin like 3 2 2
MIRT459801 POTED POTE ankyrin domain family member D 2 10
MIRT460911 POLQ DNA polymerase theta 2 2
MIRT468082 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 6
MIRT470281 PRKAA1 protein kinase AMP-activated catalytic subunit alpha 1 2 2
MIRT471876 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT476147 GPR137C G protein-coupled receptor 137C 2 8
MIRT478056 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 10
MIRT501054 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 4
MIRT501732 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT502214 HSPB8 heat shock protein family B (small) member 8 2 2
MIRT505243 UBE2D3 ubiquitin conjugating enzyme E2 D3 2 2
MIRT505957 RAN RAN, member RAS oncogene family 2 6
MIRT507996 BCL2L13 BCL2 like 13 2 4
MIRT510433 ZNF207 zinc finger protein 207 2 6
MIRT510827 SBNO1 strawberry notch homolog 1 2 4
MIRT511493 HNRNPA0 heterogeneous nuclear ribonucleoprotein A0 2 4
MIRT512129 CREBL2 cAMP responsive element binding protein like 2 2 8
MIRT514512 SHISA9 shisa family member 9 2 4
MIRT516482 RAB32 RAB32, member RAS oncogene family 2 4
MIRT519514 RBM22 RNA binding motif protein 22 2 4
MIRT523367 GTF2A1 general transcription factor IIA subunit 1 2 2
MIRT524217 DDI2 DNA damage inducible 1 homolog 2 2 6
MIRT524649 C4orf32 family with sequence similarity 241 member A 2 2
MIRT528297 ZNF76 zinc finger protein 76 2 2
MIRT528577 ITGB3BP integrin subunit beta 3 binding protein 2 2
MIRT530458 SULT1B1 sulfotransferase family 1B member 1 2 2
MIRT535774 MYCN MYCN proto-oncogene, bHLH transcription factor 2 2
MIRT544239 CCBL2 kynurenine aminotransferase 3 2 2
MIRT546733 RNF217 ring finger protein 217 2 2
MIRT550360 INCENP inner centromere protein 2 4
MIRT553343 TRPC3 transient receptor potential cation channel subfamily C member 3 2 4
MIRT556629 LAPTM4A lysosomal protein transmembrane 4 alpha 2 2
MIRT558006 FAM122B family with sequence similarity 122B 2 2
MIRT558994 CA8 carbonic anhydrase 8 2 2
MIRT560418 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2 2
MIRT565717 SESN3 sestrin 3 2 2
MIRT566271 PTAR1 protein prenyltransferase alpha subunit repeat containing 1 2 2
MIRT568161 CCDC6 coiled-coil domain containing 6 2 2
MIRT569753 C2orf71 chromosome 2 open reading frame 71 2 2
MIRT573959 FIGNL1 fidgetin like 1 2 2
MIRT574530 PEG10 paternally expressed 10 2 2
MIRT609453 CCDC149 coiled-coil domain containing 149 2 2
MIRT614047 THBS2 thrombospondin 2 2 2
MIRT628418 ATMIN ATM interactor 2 2
MIRT689556 XPO6 exportin 6 2 2
MIRT725598 CDH7 cadherin 7 2 2
MIRT735561 TRIM7 tripartite motif containing 7 3 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

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