pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-4280 |
Genomic Coordinates | chr5: 87114879 - 87114954 |
Description | Homo sapiens miR-4280 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-4280 | ||||||||||||||||||
Sequence | 11| GAGUGUAGUUCUGAGCAGAGC |31 | ||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||
Experiments | SOLiD | ||||||||||||||||||
SNPs in miRNA |
|
||||||||||||||||||
Putative Targets |
miRNA Expression profile | |
---|---|
Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | LOX | ||||||||||||||||||||
Synonyms | AAT10 | ||||||||||||||||||||
Description | lysyl oxidase | ||||||||||||||||||||
Transcript | NM_001178102 | ||||||||||||||||||||
Other Transcripts | NM_002317 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on LOX | |||||||||||||||||||||
3'UTR of LOX (miRNA target sites are highlighted) |
>LOX|NM_001178102|3'UTR 1 AAGGCAAAGCAAAACTCCCAATGGATAAATCAGTGCCTGGTGTTCTGAAGTGGGAAAAAATAGACTAACTTCAGTAGGAT 81 TTATGTATTTTGAAAAAGAGAACAGAAAACAACAAAAGAATTTTTGTTTGGACTGTTTTCAATAACAAAGCACATAACTG 161 GATTTTGAACGCTTAAGTCATCATTACTTGGGAAATTTTTAATGTTTATTATTTACATCACTTTGTGAATTAACACAGTG 241 TTTCAATTCTGTAATTACATATTTGACTCTTTCAAAGAAATCCAAATTTCTCATGTTCCTTTTGAAATTGTAGTGCAAAA 321 TGGTCAGTATTATCTAAATGAATGAGCCAAAATGACTTTGAACTGAAACTTTTCTAAAGTGCTGGAACTTTAGTGAAACA 401 TAATAATAATGGGTTTATATATGTCATAGCATAGATGAATTTAGAAACAATGCTCCTACTGTTTAAATACATATGGACAC 481 ATCTGGTGCTGAGAAAGAAACAAACACATTACCATTGGTGTCAAGAAATATTACTATATAGCAGAGAAATGGCAATACAT 561 GTACTCAGATAGTTACATCCCTATATAAAAAGTATGTTTACATTTAAAAAATTAGTAGATAACTTCCTTTCTTTCAAGTG 641 CACAATTTCATTTTGACTTGAGTCAACTTTTGTTTTGGAACAAATTAAGTAAGGGAGCTGCCCAATCCTGTCTGATATTT 721 CTTGAGGCTGCCCTCTATCATTTTATCTTTCCCATGGGCAGAGATGTTGTAAGTGGGATTCTTAATATCACCATTCTTGG 801 GACTGGTATACATAAGGCAGCCGTGAAACTGGAAAGTCATTTTGATGACTGATGTGATACATCCAGAGGTAAAATGCATT 881 TAAACATATTAAAGTATTTGCCAAAGATACAATTTTCTTGCTGACATAAAAATCACACAAACAAGTCCCCCCCAAACCAC 961 AACTGTCTCTCAAATAGCTTAAAAAAATTGAAAAACATTTTAGGATTTTTCAAGTTTTCTAGATTTTAAAAAGATGTTCA 1041 GCTATTAGAGGAATGTTAAAAATTTTATATTATCTAGAACACAGGAACATCATCCTGGGTTATTCAGGAATCAGTCACAC 1121 ATGTGTGTGTGTCTGAGATATAGTCTAAATTAGCAAAGCACATAGTATTACATACTTGAGGGGTTGGTGAACAAAGGAAA 1201 AATATACTTTCTGCAAAACCAAGGACTGTGCTGCGTAATGAGACAGCTGTGATTTCATTTGAAACTGTGAAACCATGTGC 1281 CATAATAGAATTTTGAGAATTTTGCTTTTACCTAAATTCAAGAAAATGAAATTACACTTTTAAGTTAGTGGTGCTTAAGC 1361 ATAATTTTTCCTATATTAACCAGTATTAAAATCTCAAGTAAGATTTTCCAGTGCCAGAACATGTTAGGTGGAATTTTAAA 1441 AGTGCCTCGGCATCCTGTATTACATGTCATAGAATTGTAAAGTCAACATCAATTACTAGTAATCATTCTGCACTCACTGG 1521 GTGCATAGCATGGTTAGAGGGGCTAGAGATGGACAGTCATCAACTGGCGGATATAGCGGTACATATGATCCTTAGCCACC 1601 AGGGCACAAGCTTACCAGTAGACAATACAGACAGAGCTTTTGTTGAGCTGTAACTGAGCTATGGAATAGCTTCTTTGATG 1681 TACCTCTTTGCCTTAAATTGCTTTTTAGTTCTAAGATTGTAGAATGATCCTTTCAAATTGTAATCTTTTCTAACAGAGAT 1761 ATTTTAATATACTTGCTTTCTTAAAAAACAAAAAAACTACTGTCAGTATTAATACTGAGCCAGACTGGCATCTACAGATT 1841 TCAGATCTATCATTTTATTGATTCTTAAGCTTGTATTAAAAACTAGGCAATATCATCATGGATACATAGGAGAAGACACA 1921 TTTACAATCATTCATTGGGCCTTTTATCTGTCTATCCATCCATCATCATTTGAAGGCCTAATATATGCCAAGTACTCACA 2001 TGGTATGCATTGAGACATAAAAAAGACTGTCTATAACCTCAATAAGTATTAAAAATCCCATTATTACCCATAAGGTTCAT 2081 CTTATTTCATTTTTAGGGAATAAAATTACATGTCTATGAAATTTCAATTTTAAGCACTATTGTTTTTCATGACCATAATT 2161 TATTTTTAAAAATAAATTAAAGGTTAATTATATGCATGTATGTATTTCTAATAATTAAAAATGTGTTCAATCCCTGAAAT 2241 GTCTGCCTTTTAAATATAACACCTACTATTTGGTTAATTTTGACGATTTTTTTTTTTCAATTAGGAAGCTAAAAATACTA 2321 CTTTATTCCTTATATGAACATTCATCCCCCTCCTGGCACCTCTAAACACACCCAAATAACTCACAAGTACTGATTTAACA 2401 CTCTGTATTACTGAACTTCTTTGAACTATTTTGAACTTTGAATCTCTTCTCTGAATAACTGCCGAAACTCAAAGATAATA 2481 ATTAGTTGATGAAGGTTATCAATTAATAAAATAACACAGACCAGTCTTACCAAACTCTAAATACATTTTAAAAAATAGGA 2561 ACTGGCAATGATAAAAAGAATGTTGAGTACTGACAGGAGATTGGCTTTTACACTAAAAAAGACAGAAAATGGACTAAATA 2641 GGAACATAATTTCAGAGTTTATGAGTCAGTTTACAATATGCCATATTAGCGATCTCATGATGATTCAGACCACAGTCTGG 2721 GTTAAAGATGTCTTGACCTCTGAGGCTAGCATAACATATATGAGAATACAACTTGCCTATTTCCAGAAAATCTGTATATT 2801 TTTATAGAATAACTTTATTTACAATTTCTATCATCCAATTACTCACTAGGCATTATTTGTAGTACTTTTTTTCTCTTTGA 2881 AATCTCATAGGATAGTCACACTTATAAACATTCCCAATATTCGGATTCTAGAAGAAATGCAATTCATTAAAATTTTCCTG 2961 GCACTGAGAGTTAATCTTTAGCAGATTGCATGAAAATACTGAATTCCTGGTAAGGAGATATTTTGTTTTAAAAATAATGT 3041 GTTTTGATACGAATCAGTGTATTAACTGATAACTAAAAAGTACTCTTTTTTCTATATATACATATTTTTTTGAACTCATA 3121 TTCACAATCAACATATTCAATCAGTGAGTTAAGTCTCATTCCTAGCTACCAAAATTCCTGGGCCACTTTTAAACACTAAA 3201 CATTTCATTTATCCTCTAAGCTAAAATGGTGCTGAGTTATTTAAATCTGAATGTAAAATGCATTAAATCTTAGCTTGTGG 3281 TATATAAACATTTAATTAATATAAAACTGCTTGCTATAAACTAAGTAACATGTCATTTGGTGTTAGGTTTTTAGTGAAGT 3361 TTTAGCTTCTCCCAAATTTTTCAGGAATGTTATTTGTAAGACGTGTAACTTTTTTGAAGAACTCTTATTTTAAATGCTCA 3441 GACATTGGCTTTATGTTCCTCTTTGCATTCTCATATTCTTTTATTATACATCTATACTATGATTGCAAGATTATATAAAA 3521 ATGCCTTGAATAAATGATTTCAAGTGTCAAAAAAAAAAAAAA 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 | BC-3 | ||||||
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 GSM796039. RNA binding protein: AGO2. Condition:4-Thiouridine
PAR-CLIP data was present in GSM796040. 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) |
|
||||||
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_001178102 | 3UTR | AAAAAGAAUGUUGAGUACUGACAGGAGAUUGGCUUUUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
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_002317 | 3UTR | UUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM4903835 | |
---|---|
Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_002317 | 3UTR | AAAAAGAAUGUUGAGUACUGACAGGAGAUUGGCUUUUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903836 | |
---|---|
Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_001178102 | 3UTR | AGAAUGUUGAGUACUGACAGGAGAUUGGCUUUUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM4903837 | |
---|---|
Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_001178102 | 3UTR | AGUACUGACAGGAGAUUGGCUUUUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM4903838 | |
---|---|
Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_001178102 | 3UTR | CAAUGAUAAAAAGAAUGUUGAGUACUGACAGGAGAUUGGCUUUUACACUAAAAAAGACAGAAAAUGGACUAAAUAGGAACAUAAUUUCAGAGUUUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM796039 | |
---|---|
Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | BC-3 / 4-Thiouridine |
Location of target site | ENST00000231004.4 | 3UTR | UUGGCUUUUACACUAAAAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22100165 / GSE32109 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset GSM796040 | |
---|---|
Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | BC-3 / 4-Thiouridine |
Location of target site | ENST00000231004.4 | 3UTR | UUGGCUUUUACACUAAAAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22100165 / GSE32109 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
---|---|---|---|---|---|---|---|
|
MiRNA-Target Expression Profile (TCGA) | |||||||
---|---|---|---|---|---|---|---|
|
67 hsa-miR-4280 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT065612 | DAZAP2 | DAZ associated protein 2 | 2 | 10 | ||||||||
MIRT084985 | BACH1 | BTB domain and CNC homolog 1 | 2 | 2 | ||||||||
MIRT088053 | UBXN2A | UBX domain protein 2A | 2 | 4 | ||||||||
MIRT097327 | SCAMP1 | secretory carrier membrane protein 1 | 2 | 2 | ||||||||
MIRT099148 | MYLIP | myosin regulatory light chain interacting protein | 2 | 12 | ||||||||
MIRT127042 | FAM208B | family with sequence similarity 208 member B | 2 | 4 | ||||||||
MIRT140479 | BNIP2 | BCL2 interacting protein 2 | 2 | 6 | ||||||||
MIRT154889 | GNAS | GNAS complex locus | 2 | 4 | ||||||||
MIRT187983 | MBD6 | methyl-CpG binding domain protein 6 | 2 | 2 | ||||||||
MIRT190440 | EIF5 | eukaryotic translation initiation factor 5 | 2 | 2 | ||||||||
MIRT240673 | GAPVD1 | GTPase activating protein and VPS9 domains 1 | 2 | 2 | ||||||||
MIRT295049 | EVI5L | ecotropic viral integration site 5 like | 2 | 2 | ||||||||
MIRT324749 | ACER2 | alkaline ceramidase 2 | 2 | 2 | ||||||||
MIRT366075 | FAM127A | retrotransposon Gag like 8C | 2 | 4 | ||||||||
MIRT442625 | LOX | lysyl oxidase | 2 | 2 | ||||||||
MIRT445224 | TYRP1 | tyrosinase related protein 1 | 2 | 2 | ||||||||
MIRT448967 | CCNT2 | cyclin T2 | 2 | 4 | ||||||||
MIRT450137 | PFN4 | profilin family member 4 | 2 | 2 | ||||||||
MIRT464350 | USP46 | ubiquitin specific peptidase 46 | 2 | 2 | ||||||||
MIRT470460 | PPP1R15B | protein phosphatase 1 regulatory subunit 15B | 2 | 2 | ||||||||
MIRT473691 | MAPK8 | mitogen-activated protein kinase 8 | 2 | 4 | ||||||||
MIRT480188 | CALM2 | calmodulin 2 | 2 | 6 | ||||||||
MIRT486355 | PCBD2 | pterin-4 alpha-carbinolamine dehydratase 2 | 2 | 2 | ||||||||
MIRT486708 | TROVE2 | TROVE domain family member 2 | 2 | 4 | ||||||||
MIRT488337 | SCD | stearoyl-CoA desaturase | 2 | 2 | ||||||||
MIRT489322 | PEX26 | peroxisomal biogenesis factor 26 | 2 | 2 | ||||||||
MIRT491791 | ZNF24 | zinc finger protein 24 | 2 | 2 | ||||||||
MIRT491970 | USP37 | ubiquitin specific peptidase 37 | 2 | 2 | ||||||||
MIRT492029 | TWF1 | twinfilin actin binding protein 1 | 2 | 4 | ||||||||
MIRT492063 | TMEM245 | transmembrane protein 245 | 2 | 2 | ||||||||
MIRT492247 | SLC39A9 | solute carrier family 39 member 9 | 2 | 2 | ||||||||
MIRT492254 | SLC35F5 | solute carrier family 35 member F5 | 2 | 2 | ||||||||
MIRT492592 | PPIL4 | peptidylprolyl isomerase like 4 | 2 | 2 | ||||||||
MIRT493436 | KAT7 | lysine acetyltransferase 7 | 2 | 2 | ||||||||
MIRT493470 | IPMK | inositol polyphosphate multikinase | 2 | 2 | ||||||||
MIRT493639 | HECTD1 | HECT domain E3 ubiquitin protein ligase 1 | 2 | 2 | ||||||||
MIRT493919 | FAM127B | retrotransposon Gag like 8A | 2 | 4 | ||||||||
MIRT494639 | ARNTL | aryl hydrocarbon receptor nuclear translocator like | 2 | 2 | ||||||||
MIRT500032 | ABCF2 | ATP binding cassette subfamily F member 2 | 2 | 8 | ||||||||
MIRT504589 | ADH1B | alcohol dehydrogenase 1B (class I), beta polypeptide | 2 | 4 | ||||||||
MIRT505535 | SP4 | Sp4 transcription factor | 2 | 6 | ||||||||
MIRT507539 | DNAJB6 | DnaJ heat shock protein family (Hsp40) member B6 | 2 | 6 | ||||||||
MIRT508846 | TMCO1 | transmembrane and coiled-coil domains 1 | 2 | 4 | ||||||||
MIRT510488 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | 2 | 2 | ||||||||
MIRT511402 | IFNAR2 | interferon alpha and beta receptor subunit 2 | 2 | 6 | ||||||||
MIRT523252 | HIST1H2AH | histone cluster 1 H2A family member h | 2 | 2 | ||||||||
MIRT525939 | C11orf74 | chromosome 11 open reading frame 74 | 2 | 2 | ||||||||
MIRT531453 | HSD17B12 | hydroxysteroid 17-beta dehydrogenase 12 | 2 | 2 | ||||||||
MIRT533317 | UNKL | unkempt family like zinc finger | 2 | 2 | ||||||||
MIRT541034 | STRBP | spermatid perinuclear RNA binding protein | 2 | 8 | ||||||||
MIRT546734 | RNF217 | ring finger protein 217 | 2 | 2 | ||||||||
MIRT555125 | PTPRJ | protein tyrosine phosphatase, receptor type J | 2 | 2 | ||||||||
MIRT556105 | MOAP1 | modulator of apoptosis 1 | 2 | 2 | ||||||||
MIRT560205 | AK4 | adenylate kinase 4 | 2 | 2 | ||||||||
MIRT561087 | LLPH | LLP homolog, long-term synaptic facilitation | 2 | 2 | ||||||||
MIRT566967 | LBR | lamin B receptor | 2 | 2 | ||||||||
MIRT567344 | H3F3B | H3 histone family member 3B | 2 | 2 | ||||||||
MIRT567863 | DCAF12 | DDB1 and CUL4 associated factor 12 | 2 | 2 | ||||||||
MIRT574449 | SCML2 | Scm polycomb group protein like 2 | 2 | 2 | ||||||||
MIRT575700 | Map1b | microtubule-associated protein 1B | 2 | 2 | ||||||||
MIRT651432 | YIPF6 | Yip1 domain family member 6 | 2 | 2 | ||||||||
MIRT659728 | CCDC93 | coiled-coil domain containing 93 | 2 | 2 | ||||||||
MIRT686937 | SFT2D3 | SFT2 domain containing 3 | 2 | 2 | ||||||||
MIRT699385 | SLC30A6 | solute carrier family 30 member 6 | 2 | 2 | ||||||||
MIRT710287 | CSNK1G3 | casein kinase 1 gamma 3 | 2 | 2 | ||||||||
MIRT715123 | PANK3 | pantothenate kinase 3 | 2 | 2 | ||||||||
MIRT721847 | VLDLR | very low density lipoprotein receptor | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|