Accession ID: MIRT042718 [miRNA, hsa-miR-346 :: CKB, target gene]
pre-miRNA Information
pre-miRNA ID hsa-mir-346LinkOut: [miRBase ]
Synonyms MIRN346, hsa-mir-346, miR-346, miRNA346, MIR346
Description Homo sapiens miR-346 stem-loop
Comment This sequence is the predicted human homologue . The mature miRNA differs from the rat sequence at two positions, and its expression has not been verified in human.
2nd Structure of pre-miRNA
Disease
Mature miRNA Information
Mature miRNA hsa-miR-346
Mature Sequence 20| UGUCUGCCCGCAUGCCUGCCUCU |42
Evidence Not_experimental
Experiments
Expression Profile
Putative hsa-miR-346 Targets LinkOut: [ TargetScanS 5.1 | MicroCosm | microRNA.org | miRecords | miRDB | miRo | miRNAMap 2.0 ]
Gene Information
Gene Symbol CKB LinkOut: [ Entrez Gene | BioGPS | Wikipedia | iHop ]
Synonyms B-CK, CKBB
Description creatine kinase, brain
Transcript NM_001823    LinkOut: [ RefSeq ]
Expression LinkOut: [ BioGPS ]
Putative miRNA Targets on CKB LinkOut: [ TargetScan 5.1 | MicroCosm | miRNAMap 2.0 ]
3'UTR of CKB
(miRNA target sites are highlighted)
>CKB|NM_001823|3'UTR
   1 AGCCCGGCCCACACCCGACACCAGCCCTGCTGCTTCCTAACTTATTGCCTGGGCAGTGCCCACCATGCACCCCTGATGTT
  81 CGCCGTCTGGCGAGCCCTTAGCCTTGCTGTAGAGACTTCCGTCACCCTTGGTAGAGTTTATTTTTTTGATGGCTAAGATA
 161 CTGCTGATGCTGAAATAAACTAGGGTTTTGGCCTGCCTGCGTCTG
Target sites Provided by authors  Predicted by miRanda
miRNA-target interactions (Predicted by miRanda)
IDDuplex structurePositionScoreMFE
1
miRNA  3' ucuccguccguACG--CCCGUCugu 5'
                     |||  ||||||   
Target 5' tcctaacttatTGCCTGGGCAGtgc 3'
35 - 59 110.00 -12.30
2
miRNA  3' ucuccGUCCGUACG-CCCGUCUgu 5'
               | | ||  |  ||:|||  
Target 5' gacttCCGTCACCCTTGGTAGAgt 3'
114 - 137 106.00 -5.60
3
miRNA  3' ucuccguccguACGCCCG--UCUGu 5'
                     ||  |||  |||: 
Target 5' gtttattttttTGATGGCTAAGATa 3'
136 - 160 88.00 -6.10
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target hsa-miR-346 :: CKB    [ Functional MTI ]
Validation Method CLASH
Conditions Flp-In T-REx 293-hAGO1 cells
Location of target site CDS
Original Description (Extracted from the article) ... Validation of interactions identified by CLASH suppports their reliability. ...

- Helwak, A. Kudla, G. Dudnakova, T. Tollervey, D., 2013, Cell.

Article - Helwak, A. Kudla, G. Dudnakova, T. Tollervey, D.
- Cell, 2013
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
LinkOut: [PMID: 23622248]
MiRNA-Target Expression Profile:

 
MiRNA-Target Expression Profile(TCGA):

 
MiRNA-Target Interaction Network:
Strong evidence (reporter assay, western blot, qRT-PCR or qPCR)
Other evidence
85 hsa-miR-346 Target Genes:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT000075 NRIP1 nuclear receptor interacting protein 1 1 1
MIRT000076 EFEMP2 EGF containing fibulin-like extracellular matrix protein 2 4 2
MIRT001040 LIF leukemia inhibitory factor 2 2
MIRT001128 BTK Bruton agammaglobulinemia tyrosine kinase 4 2
MIRT004219 BDH2 3-hydroxybutyrate dehydrogenase, type 2 2 1
MIRT004220 GALT galactose-1-phosphate uridylyltransferase 2 1
MIRT004221 SERHL serine hydrolase-like 2 1
MIRT004222 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2 2
MIRT004223 FNTB farnesyltransferase, CAAX box, beta 2 2
MIRT004224 GGT5 gamma-glutamyltransferase 5 2 1
MIRT004225 GJC2 gap junction protein, gamma 2, 47kDa 2 2
MIRT004226 SETD4 SET domain containing 4 2 1
MIRT004227 TSTA3 tissue specific transplantation antigen P35B 2 1
MIRT004228 CFLAR CASP8 and FADD-like apoptosis regulator 2 1
MIRT004229 SSH3 slingshot homolog 3 (Drosophila) 2 2
MIRT004230 CRELD1 cysteine-rich with EGF-like domains 1 2 1
MIRT004231 CNPY3 canopy 3 homolog (zebrafish) 2 1
MIRT004232 NR2F6 nuclear receptor subfamily 2, group F, member 6 2 1
MIRT004233 CD247 CD247 molecule 2 1
MIRT004234 TERF1 telomeric repeat binding factor (NIMA-interacting) 1 2 2
MIRT004235 RXRB retinoid X receptor, beta 2 1
MIRT004236 DGCR2 DiGeorge syndrome critical region gene 2 2 1
MIRT004237 IL11RA interleukin 11 receptor, alpha 2 1
MIRT004238 INPP5J inositol polyphosphate-5-phosphatase J 2 1
MIRT004239 MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1 2 1
MIRT004240 MED16 mediator complex subunit 16 2 1
MIRT004241 RFX1 regulatory factor X, 1 (influences HLA class II expression) 2 1
MIRT004304 IL18 interleukin 18 (interferon-gamma-inducing factor) 4 2
MIRT006669 TAP1 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 2 1
MIRT016689 ZFP36 zinc finger protein 36, C3H type, homolog (mouse) 3 1
MIRT042699 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 1 1
MIRT042700 DCAF11 DDB1 and CUL4 associated factor 11 1 1
MIRT042701 RAD54B RAD54 homolog B (S. cerevisiae) 1 1
MIRT042702 PSMD1 proteasome (prosome, macropain) 26S subunit, non-ATPase, 1 1 1
MIRT042703 EZH1 enhancer of zeste homolog 1 (Drosophila) 1 1
MIRT042704 PRDM16 PR domain containing 16 1 1
MIRT042705 GPI glucose-6-phosphate isomerase 1 1
MIRT042706 BCAP31 B-cell receptor-associated protein 31 1 1
MIRT042707 HDHD1 haloacid dehalogenase-like hydrolase domain containing 1 1 1
MIRT042708 RAD51AP1 RAD51 associated protein 1 1 1
MIRT042709 ZCCHC24 zinc finger, CCHC domain containing 24 1 1
MIRT042710 SBF1 SET binding factor 1 1 1
MIRT042711 DGCR14 DiGeorge syndrome critical region gene 14 1 1
MIRT042712 PIK3R3 phosphoinositide-3-kinase, regulatory subunit 3 (gamma) 1 1
MIRT042713 APLP2 amyloid beta (A4) precursor-like protein 2 1 1
MIRT042714 MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 1 1
MIRT042715 TEAD2 TEA domain family member 2 1 1
MIRT042716 RPL30 ribosomal protein L30 1 1
MIRT042717 FAM46A family with sequence similarity 46, member A 1 1
MIRT042718 CKB creatine kinase, brain 1 1
MIRT042719 CCHCR1 coiled-coil alpha-helical rod protein 1 1 1
MIRT042720 PRMT5 protein arginine methyltransferase 5 1 1
MIRT042721 BCOR BCL6 corepressor 1 1
MIRT042722 LIMK1 LIM domain kinase 1 1 1
MIRT042723 PSMA3 proteasome (prosome, macropain) subunit, alpha type, 3 1 1
MIRT042724 USP22 ubiquitin specific peptidase 22 1 1
MIRT042725 CNN2 calponin 2 1 1
MIRT182173 POU2F1 POU class 2 homeobox 1 1 1
MIRT437488 GSK3B glycogen synthase kinase 3 beta 3 1
MIRT471942 NR6A1 nuclear receptor subfamily 6, group A, member 1 1 1
MIRT480640 BSCL2 Berardinelli-Seip congenital lipodystrophy 2 (seipin) 1 1
MIRT504545 ZNF417 zinc finger protein 417 1 3
MIRT506772 KMT2D myeloid/lymphoid or mixed-lineage leukemia 2 1 1
MIRT512162 CD164 CD164 molecule, sialomucin 1 3
MIRT513284 PDPK1 3-phosphoinositide dependent protein kinase-1 1 2
MIRT522604 MAP7D1 MAP7 domain containing 1 1 2
MIRT531811 POLD3 polymerase (DNA-directed), delta 3, accessory subunit 1 1
MIRT575069 Ets1 E26 avian leukemia oncogene 1, 5' domain 1 1
MIRT576128 Hrk harakiri, BCL2 interacting protein (contains only BH3 domain) 1 1
MIRT606897 PPP2R1B protein phosphatase 2, regulatory subunit A, beta 1 3
MIRT608162 HRK harakiri, BCL2 interacting protein (contains only BH3 domain) 1 2
MIRT612026 FOXF2 forkhead box F2 1 1
MIRT633192 HSPE1-MOB4 HSPE1-MOB4 readthrough 1 1
MIRT634020 MOB4 MOB family member 4, phocein 1 1
MIRT646685 ASGR2 asialoglycoprotein receptor 2 1 1
MIRT680090 ETS1 v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) 1 2
MIRT688399 EMC8 ER membrane protein complex subunit 8 1 1
MIRT690848 PVR poliovirus receptor 1 1
MIRT693588 SLC39A1 solute carrier family 39 (zinc transporter), member 1 1 1
MIRT710263 FAM107A family with sequence similarity 107, member A 1 1
MIRT711309 IFNGR2 interferon gamma receptor 2 (interferon gamma transducer 1) 1 1
MIRT712871 PLEKHG4 pleckstrin homology domain containing, family G (with RhoGef domain) member 4 1 1
MIRT717684 PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) 1 1
MIRT721355 ENTHD1 ENTH domain containing 1 1 1
MIRT722562 C1orf95 chromosome 1 open reading frame 95 1 1
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