pre-miRNA Information | |
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pre-miRNA | hsa-mir-3160-1 |
Genomic Coordinates | chr11: 46451805 - 46451889 |
Description | Homo sapiens miR-3160-1 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | hsa-mir-3160-2 |
Genomic Coordinates | chr11: 46451807 - 46451887 |
Description | Homo sapiens miR-3160-2 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3160-3p | ||||||||||||||||||||||||||||||
Sequence | 54| AGAGCUGAGACUAGAAAGCCCA |75 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Illumina | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TFCP2 | ||||||||||||||||||||
Synonyms | LBP1C, LSF, LSF1D, SEF, TFCP2C | ||||||||||||||||||||
Description | transcription factor CP2 | ||||||||||||||||||||
Transcript | NM_001173452 | ||||||||||||||||||||
Other Transcripts | NM_001173453 , NM_005653 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TFCP2 | |||||||||||||||||||||
3'UTR of TFCP2 (miRNA target sites are highlighted) |
>TFCP2|NM_001173452|3'UTR 1 GAGTGCGGCGTTTCGTGCCCAGTGGCTGCTCCTTCCTTCACCTCTGAAAACGGCCCTCTTGAAGGGGGATATGAATGGAG 81 ATTTGAAGGTCTGCAAGAACCTGACTCGTCTGACTGTGTGTGGAGGAGTCCAGGCCATGGAGGCAGAATCCTGGCCCTCT 161 GTGTTGGCCCAAGCTCTTGTGGTACACACAGATTACTGCCCAATATGCAGTTCTGCAGCTGTTTTAGTTAAATTTCTGGA 241 CCTTGTTGTTGTTAAATATCAGTAGAAACTCTACATAATTTAGAGTGTATGTAGGGCATAATGATGATGGGAATTGTGTG 321 ATGTTTAACAGGAAGATCTTAAATTTTGTGATATGGAGCCCTGTAATTTTTTTCTTATATAAAAATGGGTATCTATATTC 401 ATAAGACTAGGTCTTCAATCTCTTTGTACTGGTCTCAAATGTACTGGTATCTCTGCTTTTTGCCACAGTTTGTCCCTGAA 481 AACTTTATCAGTGAGGAGAAATACAGAATTTTCCTTTTGGTTCCCCTGTAATACCACAACTAATAGTATTTTCAGCTAAC 561 ATTTATTGACCAGGCAGTGTGATAAATTTTTTGAATGACCATCTTGTTTAACCCCCTAATCACACTATCTGAAGTAGGTG 641 CTATAGTGACCCCCAACCGAAGATGAGGAAATGGAGACACACAGTGGCTAAGTAGCTTGCTAGGTGCCAGGAGCTGGCAG 721 GCAGTGATGCTGAAATCCAAACCAGGCAATCTGGCCCTCCTTATTCACCCTCTCATACCACCAGTGCTACCCATTATAAC 801 CTGTGTTCACTTCGCTTATTACTGTGGCCCTTCTGGTGACTACAACATAACACTGAGTATGAACTGAGGAATTAACCACT 881 GAAAGAGACAAAGCACACCTAAATAATGATGAACAAATCAAGACCTACAAGAAATGAACACATAGATGCTTTTTAAGTGT 961 CATTAGTTATCGGAATCAAAGAATTTGAGGTGGTGACAACTGGGGATTATCTGTAACTCCCCAAATTTACTGTTCTTGAA 1041 TGACATTCTCAAACTATTTATTAATGAGTTAGTCTCATCCCTGCTTTCTGTTTCCTCTCTCTGCATCTTCTCTTGGCATA 1121 GGAAGTTATTTTACTCATGCTATGTTTTTTAATAGAAGCTTTACAAAAAAAGATGCATTCCCTTCCTGTTCACACTCTTA 1201 CCATGTTTTTGTTCTTCCTTAAGAATGATTGTGTGTGTGTGTGTGTGTGTGTGTAAGTGTGTAAGTGTAACATCATGGGT 1281 TTTCTTTCTTCACTTGTAAAGTTTTATCTAGAAATACTTTTACAGGTTATGTTGAGGTACACAAAGATAATGTTCTAAGA 1361 TTGTGTATTGGATTTGGATTTGTGTGTGTGTGTGTGTGTGTGTGTGTTTAAAGCATTTGATAAGGTTTAAATGTTTTTTA 1441 TACAGAGATTTTTGTTCATTAAACTCAATCTGCATCATGGTCTAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293/HeLa | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM1067870. RNA binding protein: AGO2. Condition:Ago2 IP-seq (mitotic cells)
... - Kishore S; Gruber AR; Jedlinski DJ; Syed et al., 2013, Genome biology. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Gruber AR; Jedlinski DJ; Syed et al. - Genome biology, 2013
BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
LinkOut: [PMID: 23706177]
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CLIP-seq Support 1 for dataset GSM1067870 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293/HeLa / Ago2 IP-seq (mitotic cells) |
Location of target site | ENST00000257915.5 | 3UTR | ACUUGCAACCUCUGCCUC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23706177 / GSE43666 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||
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118 hsa-miR-3160-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT066658 | DYRK2 | dual specificity tyrosine phosphorylation regulated kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT075318 | SF3B3 | splicing factor 3b subunit 3 | ![]() |
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2 | 4 | ||||||
MIRT077083 | EIF1 | eukaryotic translation initiation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT100381 | HSPA1B | heat shock protein family A (Hsp70) member 1B | ![]() |
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2 | 6 | ||||||
MIRT135259 | TMBIM6 | transmembrane BAX inhibitor motif containing 6 | ![]() |
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2 | 4 | ||||||
MIRT184913 | ZNF268 | zinc finger protein 268 | ![]() |
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2 | 2 | ||||||
MIRT218862 | CDKN1A | cyclin dependent kinase inhibitor 1A | ![]() |
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2 | 2 | ||||||
MIRT446580 | FPR2 | formyl peptide receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT448834 | FGD4 | FYVE, RhoGEF and PH domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT449455 | RNF13 | ring finger protein 13 | ![]() |
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2 | 2 | ||||||
MIRT452284 | CARD8 | caspase recruitment domain family member 8 | ![]() |
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2 | 2 | ||||||
MIRT452628 | FAM162A | family with sequence similarity 162 member A | ![]() |
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2 | 2 | ||||||
MIRT453454 | GLG1 | golgi glycoprotein 1 | ![]() |
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2 | 2 | ||||||
MIRT454188 | AP1S3 | adaptor related protein complex 1 sigma 3 subunit | ![]() |
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2 | 6 | ||||||
MIRT454434 | GTF2F1 | general transcription factor IIF subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT454575 | NT5DC3 | 5'-nucleotidase domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT455555 | TRAF1 | TNF receptor associated factor 1 | ![]() |
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2 | 6 | ||||||
MIRT455841 | MPL | MPL proto-oncogene, thrombopoietin receptor | ![]() |
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2 | 6 | ||||||
MIRT455969 | BCAS4 | breast carcinoma amplified sequence 4 | ![]() |
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2 | 4 | ||||||
MIRT456805 | SIGLEC14 | sialic acid binding Ig like lectin 14 | ![]() |
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2 | 2 | ||||||
MIRT457320 | DUSP19 | dual specificity phosphatase 19 | ![]() |
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2 | 2 | ||||||
MIRT457366 | POFUT2 | protein O-fucosyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT457684 | ZNF587 | zinc finger protein 587 | ![]() |
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2 | 2 | ||||||
MIRT458158 | LYRM4 | LYR motif containing 4 | ![]() |
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2 | 6 | ||||||
MIRT458641 | SGPP2 | sphingosine-1-phosphate phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT459134 | FADS6 | fatty acid desaturase 6 | ![]() |
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2 | 2 | ||||||
MIRT459153 | NARF | nuclear prelamin A recognition factor | ![]() |
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2 | 4 | ||||||
MIRT460460 | NOM1 | nucleolar protein with MIF4G domain 1 | ![]() |
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2 | 4 | ||||||
MIRT460974 | STK17B | serine/threonine kinase 17b | ![]() |
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2 | 2 | ||||||
MIRT461439 | ACSBG1 | acyl-CoA synthetase bubblegum family member 1 | ![]() |
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2 | 2 | ||||||
MIRT461507 | NEDD4L | neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase | ![]() |
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2 | 2 | ||||||
MIRT462490 | GSR | glutathione-disulfide reductase | ![]() |
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2 | 2 | ||||||
MIRT462638 | PHF5A | PHD finger protein 5A | ![]() |
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2 | 2 | ||||||
MIRT463279 | ZFX | zinc finger protein, X-linked | ![]() |
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2 | 2 | ||||||
MIRT463360 | ZFAND4 | zinc finger AN1-type containing 4 | ![]() |
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2 | 2 | ||||||
MIRT465777 | TMOD3 | tropomodulin 3 | ![]() |
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2 | 2 | ||||||
MIRT466143 | TMEM120B | transmembrane protein 120B | ![]() |
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2 | 2 | ||||||
MIRT468401 | SETD3 | SET domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT468998 | RNPS1 | RNA binding protein with serine rich domain 1 | ![]() |
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2 | 2 | ||||||
MIRT471574 | PARD6B | par-6 family cell polarity regulator beta | ![]() |
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2 | 2 | ||||||
MIRT472108 | NME2 | NME/NM23 nucleoside diphosphate kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT472125 | NME1-NME2 | NME1-NME2 readthrough | ![]() |
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2 | 2 | ||||||
MIRT473020 | MRPS14 | mitochondrial ribosomal protein S14 | ![]() |
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2 | 2 | ||||||
MIRT473083 | MORN4 | MORN repeat containing 4 | ![]() |
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2 | 2 | ||||||
MIRT475598 | HMGB2 | high mobility group box 2 | ![]() |
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2 | 4 | ||||||
MIRT475937 | GXYLT2 | glucoside xylosyltransferase 2 | ![]() |
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2 | 8 | ||||||
MIRT476117 | GPR157 | G protein-coupled receptor 157 | ![]() |
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2 | 2 | ||||||
MIRT476406 | GDE1 | glycerophosphodiester phosphodiesterase 1 | ![]() |
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2 | 2 | ||||||
MIRT478003 | DNAL1 | dynein axonemal light chain 1 | ![]() |
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2 | 2 | ||||||
MIRT487969 | IQSEC2 | IQ motif and Sec7 domain 2 | ![]() |
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2 | 2 | ||||||
MIRT489418 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT491522 | IL10RA | interleukin 10 receptor subunit alpha | ![]() |
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2 | 2 | ||||||
MIRT492673 | PLEC | plectin | ![]() |
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2 | 2 | ||||||
MIRT493545 | ICOSLG | inducible T-cell costimulator ligand | ![]() |
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2 | 2 | ||||||
MIRT513085 | USP9X | ubiquitin specific peptidase 9, X-linked | ![]() |
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2 | 2 | ||||||
MIRT514009 | CECR2 | CECR2, histone acetyl-lysine reader | ![]() |
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2 | 4 | ||||||
MIRT516683 | ZNF860 | zinc finger protein 860 | ![]() |
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2 | 2 | ||||||
MIRT518392 | ZNF250 | zinc finger protein 250 | ![]() |
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2 | 2 | ||||||
MIRT522683 | LUZP1 | leucine zipper protein 1 | ![]() |
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2 | 6 | ||||||
MIRT524488 | CEP97 | centrosomal protein 97 | ![]() |
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2 | 2 | ||||||
MIRT527457 | CLEC12B | C-type lectin domain family 12 member B | ![]() |
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2 | 2 | ||||||
MIRT527705 | IL17REL | interleukin 17 receptor E like | ![]() |
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2 | 2 | ||||||
MIRT531647 | C19orf52 | translocase of inner mitochondrial membrane 29 | ![]() |
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2 | 2 | ||||||
MIRT532381 | UMPS | uridine monophosphate synthetase | ![]() |
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2 | 2 | ||||||
MIRT532588 | MTHFD1 | methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 | ![]() |
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2 | 2 | ||||||
MIRT533555 | TPM4 | tropomyosin 4 | ![]() |
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2 | 2 | ||||||
MIRT548371 | ENTPD5 | ectonucleoside triphosphate diphosphohydrolase 5 | ![]() |
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2 | 4 | ||||||
MIRT550250 | PVR | poliovirus receptor | ![]() |
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2 | 2 | ||||||
MIRT552555 | ZFP36L2 | ZFP36 ring finger protein like 2 | ![]() |
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2 | 4 | ||||||
MIRT554113 | SMARCE1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 | ![]() |
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2 | 2 | ||||||
MIRT554131 | SMARCA5 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 | ![]() |
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2 | 2 | ||||||
MIRT561344 | ZBTB18 | zinc finger and BTB domain containing 18 | ![]() |
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2 | 2 | ||||||
MIRT561638 | RUNX3 | runt related transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT566497 | PBX2P1 | PBX homeobox 2 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT570583 | OTUD7B | OTU deubiquitinase 7B | ![]() |
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2 | 2 | ||||||
MIRT572731 | MCTS1 | MCTS1, re-initiation and release factor | ![]() |
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2 | 2 | ||||||
MIRT574041 | PEX26 | peroxisomal biogenesis factor 26 | ![]() |
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2 | 2 | ||||||
MIRT575231 | Fut1 | fucosyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT606811 | BICD2 | BICD cargo adaptor 2 | ![]() |
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2 | 2 | ||||||
MIRT621016 | CLSTN3 | calsyntenin 3 | ![]() |
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2 | 2 | ||||||
MIRT637852 | PDCL3 | phosducin like 3 | ![]() |
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2 | 2 | ||||||
MIRT640477 | ZNF557 | zinc finger protein 557 | ![]() |
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2 | 2 | ||||||
MIRT642827 | LINC00346 | long intergenic non-protein coding RNA 346 | ![]() |
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2 | 2 | ||||||
MIRT643887 | IMP4 | IMP4, U3 small nucleolar ribonucleoprotein | ![]() |
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2 | 2 | ||||||
MIRT664874 | PCNXL2 | pecanex homolog 2 | ![]() |
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2 | 2 | ||||||
MIRT680528 | PRIM2 | DNA primase subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT680648 | KIAA1456 | KIAA1456 | ![]() |
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2 | 2 | ||||||
MIRT680807 | ZNF578 | zinc finger protein 578 | ![]() |
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2 | 2 | ||||||
MIRT680921 | STX2 | syntaxin 2 | ![]() |
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2 | 2 | ||||||
MIRT681112 | CEP57L1 | centrosomal protein 57 like 1 | ![]() |
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2 | 2 | ||||||
MIRT681147 | INTS7 | integrator complex subunit 7 | ![]() |
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2 | 2 | ||||||
MIRT681966 | TFCP2 | transcription factor CP2 | ![]() |
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2 | 2 | ||||||
MIRT684316 | GTF3C4 | general transcription factor IIIC subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT684906 | GSG2 | histone H3 associated protein kinase | ![]() |
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2 | 2 | ||||||
MIRT685499 | MED16 | mediator complex subunit 16 | ![]() |
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2 | 2 | ||||||
MIRT685929 | MOCS3 | molybdenum cofactor synthesis 3 | ![]() |
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2 | 2 | ||||||
MIRT686875 | SLC25A32 | solute carrier family 25 member 32 | ![]() |
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2 | 2 | ||||||
MIRT688204 | FNIP1 | folliculin interacting protein 1 | ![]() |
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2 | 2 | ||||||
MIRT688791 | CCNB1 | cyclin B1 | ![]() |
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2 | 2 | ||||||
MIRT689227 | RPS19 | ribosomal protein S19 | ![]() |
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2 | 2 | ||||||
MIRT690470 | ZNF33A | zinc finger protein 33A | ![]() |
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2 | 2 | ||||||
MIRT691982 | PLCXD1 | phosphatidylinositol specific phospholipase C X domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT694006 | PPIL4 | peptidylprolyl isomerase like 4 | ![]() |
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2 | 2 | ||||||
MIRT694529 | TRIM72 | tripartite motif containing 72 | ![]() |
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2 | 2 | ||||||
MIRT695420 | ADH5 | alcohol dehydrogenase 5 (class III), chi polypeptide | ![]() |
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2 | 2 | ||||||
MIRT695784 | HSD17B12 | hydroxysteroid 17-beta dehydrogenase 12 | ![]() |
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2 | 2 | ||||||
MIRT697799 | UBXN2A | UBX domain protein 2A | ![]() |
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2 | 2 | ||||||
MIRT698275 | TMEM2 | transmembrane protein 2 | ![]() |
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2 | 2 | ||||||
MIRT698317 | TMEM136 | transmembrane protein 136 | ![]() |
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2 | 2 | ||||||
MIRT699971 | RREB1 | ras responsive element binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT700717 | PNO1 | partner of NOB1 homolog | ![]() |
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2 | 2 | ||||||
MIRT701721 | MTMR12 | myotubularin related protein 12 | ![]() |
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2 | 2 | ||||||
MIRT701879 | MPLKIP | M-phase specific PLK1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT702959 | HIF1A | hypoxia inducible factor 1 alpha subunit | ![]() |
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2 | 2 | ||||||
MIRT706178 | ZNF716 | zinc finger protein 716 | ![]() |
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2 | 2 | ||||||
MIRT706463 | SPRED1 | sprouty related EVH1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT718154 | TTC33 | tetratricopeptide repeat domain 33 | ![]() |
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2 | 2 | ||||||
MIRT718711 | ANKRD18A | ankyrin repeat domain 18A | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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