pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-2115 |
Genomic Coordinates | chr3: 48316360 - 48316459 |
Description | Homo sapiens miR-2115 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-2115-3p | |||||||||
Sequence | 58| CAUCAGAAUUCAUGGAGGCUAG |79 | |||||||||
Evidence | Experimental | |||||||||
Experiments | 454 | DRVs in miRNA |
|
|||||||
SNPs in miRNA |
|
|||||||||
Putative Targets |
miRNA Expression profile | |
---|---|
miRNAs in Extracellular Vesicles |
|
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | GALNT4 | ||||||||||||||||||||
Synonyms | GALNAC-T4, GALNACT4 | ||||||||||||||||||||
Description | polypeptide N-acetylgalactosaminyltransferase 4 | ||||||||||||||||||||
Transcript | NM_003774 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on GALNT4 | |||||||||||||||||||||
3'UTR of GALNT4 (miRNA target sites are highlighted) |
>GALNT4|NM_003774|3'UTR 1 AGCACAACAGCACTTTCGTCATGAGCTGACAGTAGTGTCAAGAAAGTCAAAGAGCCTTAAGAGCCTCAGTGAAGATTGTA 81 TTTTATTTTATCAAAAGCCACCTAGCAGTCATCTGTGGAGCACTGGAAAGCTGGGGTTCATTTTGGTATATCACACTGAA 161 ACTGGGTACCCAGAGTGCTGCTGTTTAATATTTCACAATGCCTTACTTATTGGTTGTTTTATATAAGAGTTTTGTCAATA 241 TGGTCTCTTCTTAAAAGAAGTTGACTATGAATTGAAACACACAAAACATTTAAGTGCCAGACTTAATATTAAAGAATGTA 321 AAGGTCCAAGTAAAATGAGGTATGATTTATGTTGATGTGTAAGTTCACCGCACATCCCACTTTTTAACAAAACTCATGAA 401 TGTGCAGTTTGAGCCATTGCTATTTTGATTACATAGAATTTGTATTTCTTTTTTAGCCAGCACATTAAATTTTAGATTTT 481 ATTTTTTAATCTAATTTTTTTCTAATCAAAAAGAAAATTGAGCTTAAGGCAAAAGGCCTGGTTTTAGAGATATGTGTAAT 561 TGGAAGAGGGCATTTGTTTGAGTGTGAGTTTGGAGGCCTTTTTAACATGCAGACATACCCATATTTAAATGAAATGGGGA 641 GATATTTACATTCCGTACTTTGTAAACTTGAGCTATTGGACTTCACTGATGTATATATTAATACCTCAGATTCCTCTGAT 721 TTTGTAAGCTGTCTTCTCTGTGAACGTGTTTGTGTGTGTAGGGCATTTTCTGATTGCACTTCCTTAAGTTATGAATGTAC 801 TAGAAAGGGACTCATCCAGAATACTATGCCTCCCTTTGTTAATGCTTAATCATTTAAAGTAAACACAATTGAAGCCTCTC 881 TGAAGTTAAACCCAACTATGTTTATTAAAATGTGTGAAACTGAAAGTGGGCTAGGTTCTACCAAGGCTGTGGAACTCTCC 961 TACGAGTTCTGCTGATCAGGAAATTTAAGAATTTATCTTAAAAATGCAAGGAAAAAAGACTGCCTTGGCAATTGTGAATG 1041 GTGCTTTCAATCTCCTAGCACCGAGCCTGGCACTTAGGCAGCTTTCAGTAAGTGGGTGAATGAATGACTGAATGAATGAA 1121 TGAATGGCTCAGCTGAGGAATGTAACTTTGGTCAAGTTATTATGATGTGTTTGGGCTTAGTTTTCTCATTGGTAAAATGT 1201 GGGTGCTGGATTGGATCTTAAAGATCCCTTCCAGCTCTGAAATGCTGATTGTACAGTATATTCTTCCCAGATTGACTCAC 1281 TGTGCAATCTTTACAATACTTTTTATCTTTTCACTTTTGACATAGGTAATGTTGTTGAGCAGTTGAGCAATGTTCAGTCC 1361 AGTTGTGAAGCTGGAGAAGAGAAATGGGTTTTAAAAATTAAGTGAGGGGAGGCCGGGTGCGGTGGCTCACGCATGTAATC 1441 CCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACGAGGTCAGGAGATCCAGACCATCCTGGCTAACATGGTGAAACCTCG 1521 TCTCTACTAAAAATACAAAAAATTAGCCAGCTGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGG 1601 AGAATGGCGTGAACCTGTGAGGCAGAGCTTACAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGCAA 1681 GACTCTGTCTCAAAAAAAAAAAATAATAATAAAATAAGTGAGCTGAACTCACCTGAAGTGGTTTACTTCTGTGGGTTAAG 1761 AAGTTCTAGTCAGTGTTCATAGTCGTTTCGTTTTGATAATTGTTGAACCAATTTTGTTTTTAAAACCTTTAGACTCTGAA 1841 AGTAATATTTTGACTAAGAATGTAAATATTTCCAAACTAAATTACTCGGGAAGTAAACGCTTTTTTTAAAAGTATTTTTA 1921 CTGGTTTTATACCAATATTATATGCAGAAATCACAGGATGAATTTAGAATTAAATCTCAATTAGTTCACTTTGGCCTAGA 2001 TTTATGAAAAATGCATGCCTCGTAAAGAGTCCACTGTATTCACGAGTAAAGTTGCTTTTAGTGTTCACTTGATGACTTGG 2081 AGAGTAGGAATTTTGCAAAATCTGAATTTAAGGAAATTCTTTAGGATAACCATTTCAAAAAATAAAATTGCTATGCAATC 2161 TTGAATATTTTCTCTTTTGCCTCGTAAAATGAAAATGCATTCACAGTTTCTGTAAATTATTTAGCAGCCTTAAAGTTTAT 2241 CAAAAAATTGTCCAGATTCCACGTGCAGCATGCTTGGCCCTGCATTTAATTTAAGAAGGATTAATAATAATGCTCTGAAT 2321 TTTTCGAAAGGGATTCTCCTAAACCCACCCACTTCTCTTGCCCAGGCTGCTTTTTAAAAATATTTTTTTATTTTTTACTT 2401 ATTTTTAAATTTTCTCTTTTTATTTATTTTTGGTTTTCTTGTTAGCCACCTGTTATATGGGAGAACGAAAATTGTTATAT 2481 TTTGAAAGTACTTATTACATTATTTTTATTTTAGTATCTTGATGCTCCTGTCAAAAGGGAAATGAGGCTTTTAAAAATAA 2561 AGTACCTTAATTCTTTATTGACTTTTTGCCCTAAATTGCTAGGTGTGACCCAGCAATCTTTTAGGAAGAGATTTTACAGT 2641 GGTGCTTTATTTATATCAATAATCCAGTATAGTTAGGCTGTTCATTCCTCATAATAGAGTACATAACAGAAAAGTGGGAC 2721 TTTCACATTTTCATATTTAGGCACGTTCCAATTTAATTCCAAAAATACTCTGTAATTCTACATCTAAAAAAACCGATTCC 2801 CTAATTCGAATTTATTGGTACCAAAGCTCTCTTTGGCTATAGACAATTAAGAGTTGACCTTTTAAGTTAATGTATATGCT 2881 TAAAAACAGTTTTAGGAAAATATTTGGTAGACAAAGAGTTTCAACTTTAAATGTTCACTATGTCATTTAGTGTCCAACTT 2961 TACGGATAGGTTGACTATCTAAATAGGCATTTTTAGTCATTAAAAAAAATCTAGTCACCAGGAGGATCCCTATAACTCAA 3041 AATAACTTGTTTGTAAAAGAAAATTTGTTTACTTACCCATTAGTAAGTTCCTGCATATTCATTATAAGATGGCAAATCAA 3121 ACTTTTCTAGGATGAAGACAGCTTATTTTTAAGTTGTATAGTCTTAGTTGGTTTAGGGTCTCAATTTTAATTAATAAAAT 3201 ACTTGGTTTTTATTTGCTTGTCCTTTTGAATTCCTGTTTTAATAATTTTAAAATGAGCACAAAGAACGTTGAAGTTCAGA 3281 TTAATCTCTTCTGAATGATGTTTTTTTCCTCTGTGATGAGTTGTTTCTGACTTTTTTCCTTTTGTATTTGTAATGTTGAT 3361 TAAGATGTAAAATAAAAAGTGTGCCTGATTATTTTTGCAAAAAAAAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
|
||||||||||||||||||||
miRNA-target interactions (Predicted by miRanda) |
|
||||||||||||||||||||
DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
---|---|
miRNA:Target | ---- |
Validation Method |
|
Conditions | MCF7 |
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
|
CLIP-seq Support 1 for dataset SRR1045082 | |
---|---|
Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000529983.2 | 3UTR | CAUUUUCUGAUUGCACUUCCUUAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
---|---|---|---|---|---|---|---|
|
MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
80 hsa-miR-2115-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
![]() |
![]() |
|||||||
Strong evidence | Less strong evidence | |||||||||||
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
|||||
MIRT057089 | DDIT4 | DNA damage inducible transcript 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT071216 | FCF1 | FCF1, rRNA-processing protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT226901 | RAD23B | RAD23 homolog B, nucleotide excision repair protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT235961 | BACH1 | BTB domain and CNC homolog 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT294569 | ZNF460 | zinc finger protein 460 | ![]() |
![]() |
2 | 4 | ||||||
MIRT321046 | RAC1 | Rac family small GTPase 1 | ![]() |
![]() |
2 | 4 | ||||||
MIRT359666 | NUS1 | NUS1 dehydrodolichyl diphosphate synthase subunit | ![]() |
![]() |
2 | 8 | ||||||
MIRT366451 | KLHL15 | kelch like family member 15 | ![]() |
![]() |
2 | 2 | ||||||
MIRT405375 | ZBTB18 | zinc finger and BTB domain containing 18 | ![]() |
![]() |
2 | 2 | ||||||
MIRT441794 | TCEAL5 | transcription elongation factor A like 5 | ![]() |
![]() |
2 | 2 | ||||||
MIRT443295 | TCEAL3 | transcription elongation factor A like 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT455275 | DDX39B | DExD-box helicase 39B | ![]() |
![]() |
2 | 2 | ||||||
MIRT458523 | C5orf22 | chromosome 5 open reading frame 22 | ![]() |
![]() |
2 | 2 | ||||||
MIRT464960 | TWIST1 | twist family bHLH transcription factor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT466848 | STX6 | syntaxin 6 | ![]() |
![]() |
2 | 2 | ||||||
MIRT469252 | RHOB | ras homolog family member B | ![]() |
![]() |
2 | 2 | ||||||
MIRT469825 | RAB14 | RAB14, member RAS oncogene family | ![]() |
![]() |
2 | 4 | ||||||
MIRT470047 | PTGFRN | prostaglandin F2 receptor inhibitor | ![]() |
![]() |
2 | 2 | ||||||
MIRT471420 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT472024 | NPM1 | nucleophosmin 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT484156 | CENPN | centromere protein N | ![]() |
![]() |
2 | 2 | ||||||
MIRT485490 | HMGN2 | high mobility group nucleosomal binding domain 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT490462 | PROSER2 | proline and serine rich 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT493069 | MTCH1 | mitochondrial carrier 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT493573 | HSP90AA1 | heat shock protein 90 alpha family class A member 1 | ![]() |
![]() |
2 | 8 | ||||||
MIRT494919 | NDUFC2-KCTD14 | NDUFC2-KCTD14 readthrough | ![]() |
![]() |
2 | 2 | ||||||
MIRT500439 | ZMAT3 | zinc finger matrin-type 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT500931 | SRPR | SRP receptor alpha subunit | ![]() |
![]() |
2 | 4 | ||||||
MIRT501551 | POC1B-GALNT4 | POC1B-GALNT4 readthrough | ![]() |
![]() |
2 | 2 | ||||||
MIRT501809 | NEURL1B | neuralized E3 ubiquitin protein ligase 1B | ![]() |
![]() |
2 | 2 | ||||||
MIRT502415 | GALNT4 | polypeptide N-acetylgalactosaminyltransferase 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT506504 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
![]() |
2 | 2 | ||||||
MIRT507861 | CCNE2 | cyclin E2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT510511 | YOD1 | YOD1 deubiquitinase | ![]() |
![]() |
2 | 6 | ||||||
MIRT516073 | RAB42 | RAB42, member RAS oncogene family | ![]() |
![]() |
2 | 2 | ||||||
MIRT519030 | KYNU | kynureninase | ![]() |
![]() |
2 | 6 | ||||||
MIRT521762 | PPIL1 | peptidylprolyl isomerase like 1 | ![]() |
![]() |
2 | 4 | ||||||
MIRT522898 | KCNJ3 | potassium voltage-gated channel subfamily J member 3 | ![]() |
![]() |
2 | 4 | ||||||
MIRT527370 | MGARP | mitochondria localized glutamic acid rich protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT530691 | C8orf46 | chromosome 8 open reading frame 46 | ![]() |
![]() |
2 | 2 | ||||||
MIRT530867 | TRUB1 | TruB pseudouridine synthase family member 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT531832 | MTPAP | mitochondrial poly(A) polymerase | ![]() |
![]() |
2 | 4 | ||||||
MIRT533035 | ZBTB5 | zinc finger and BTB domain containing 5 | ![]() |
![]() |
2 | 2 | ||||||
MIRT533165 | WIPF2 | WAS/WASL interacting protein family member 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT533464 | TRIM71 | tripartite motif containing 71 | ![]() |
![]() |
2 | 2 | ||||||
MIRT534331 | SHCBP1 | SHC binding and spindle associated 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT539372 | ADSS | adenylosuccinate synthase | ![]() |
![]() |
2 | 6 | ||||||
MIRT545951 | ZBTB10 | zinc finger and BTB domain containing 10 | ![]() |
![]() |
2 | 2 | ||||||
MIRT553283 | TSR1 | TSR1, ribosome maturation factor | ![]() |
![]() |
2 | 2 | ||||||
MIRT553532 | TMEM185B | transmembrane protein 185B | ![]() |
![]() |
2 | 4 | ||||||
MIRT556480 | LIPA | lipase A, lysosomal acid type | ![]() |
![]() |
2 | 2 | ||||||
MIRT556975 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
![]() |
2 | 2 | ||||||
MIRT557697 | GATA6 | GATA binding protein 6 | ![]() |
![]() |
2 | 2 | ||||||
MIRT558901 | CCDC58 | coiled-coil domain containing 58 | ![]() |
![]() |
2 | 2 | ||||||
MIRT559224 | BLMH | bleomycin hydrolase | ![]() |
![]() |
2 | 2 | ||||||
MIRT559827 | SLPI | secretory leukocyte peptidase inhibitor | ![]() |
![]() |
2 | 2 | ||||||
MIRT563435 | SLC3A2 | solute carrier family 3 member 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT569270 | PCDH11X | protocadherin 11 X-linked | ![]() |
![]() |
2 | 2 | ||||||
MIRT571386 | JKAMP | JNK1/MAPK8-associated membrane protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT572567 | AFF1 | AF4/FMR2 family member 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT610400 | AR | androgen receptor | ![]() |
![]() |
2 | 2 | ||||||
MIRT611058 | ZNF621 | zinc finger protein 621 | ![]() |
![]() |
2 | 2 | ||||||
MIRT635118 | TMEM233 | transmembrane protein 233 | ![]() |
![]() |
2 | 2 | ||||||
MIRT641617 | DEFB118 | defensin beta 118 | ![]() |
![]() |
2 | 2 | ||||||
MIRT642146 | CHORDC1 | cysteine and histidine rich domain containing 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT647295 | C8orf33 | chromosome 8 open reading frame 33 | ![]() |
![]() |
2 | 2 | ||||||
MIRT648155 | MPLKIP | M-phase specific PLK1 interacting protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT652780 | TENM3 | teneurin transmembrane protein 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT657356 | HNRNPA2B1 | heterogeneous nuclear ribonucleoprotein A2/B1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT658718 | ELN | elastin | ![]() |
![]() |
2 | 2 | ||||||
MIRT662441 | RALGAPA1 | Ral GTPase activating protein catalytic alpha subunit 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT665302 | ZBTB38 | zinc finger and BTB domain containing 38 | ![]() |
![]() |
2 | 2 | ||||||
MIRT699898 | RUNX1 | runt related transcription factor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT700921 | PDS5A | PDS5 cohesin associated factor A | ![]() |
![]() |
2 | 2 | ||||||
MIRT700992 | PDE3A | phosphodiesterase 3A | ![]() |
![]() |
2 | 2 | ||||||
MIRT707397 | DCAF4L1 | DDB1 and CUL4 associated factor 4 like 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT711895 | INSIG2 | insulin induced gene 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT712072 | XRCC5 | X-ray repair cross complementing 5 | ![]() |
![]() |
2 | 2 | ||||||
MIRT716121 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT724470 | SMAD2 | SMAD family member 2 | ![]() |
![]() |
2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|