miRTarBase - #MIRT576346


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pre-miRNA Information
pre-miRNA hsa-mir-628   
Genomic Coordinates chr15: 55372940 - 55373034
Synonyms MIRN628, hsa-mir-628, MIR628
Description Homo sapiens miR-628 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-628-5p
Sequence 23| AUGCUGACAUAUUUACUAGAGG |44
Evidence Experimental
Experiments Cloned
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN15665015 15 COSMIC
COSN30467735 21 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs761527552 8 dbSNP
rs776423775 9 dbSNP
rs200771662 11 dbSNP
rs760615166 12 dbSNP
rs747172385 13 dbSNP
rs775387693 16 dbSNP
rs771606673 19 dbSNP
rs745373506 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Gene Information
Gene Symbol Pxdn   
Synonyms 2310075M15Rik, C85409, E330004E07, VPO1, mKIAA0230
Description peroxidasin
Transcript NM_181395   
Expression
Putative miRNA Targets on Pxdn
3'UTR of Pxdn
(miRNA target sites are highlighted)		 
>Pxdn|NM_181395|3'UTR
   1 TGTTCCCGAGCTTAGCTCCTCGAAGCTGGTCCACAGAATACTTGTGAGCCTAGATGACAACATGGGGAGCTTCAGACCAC
  81 AGGACAAGTTGGGATCTCAGACATTTCAGGACCTCTGCTGTGCCATCGCAGAAGCAGCCGGGGCTGCTTCACACCCTGTG
 161 TTTGTAGAAGGAAATTGAGCAGGCGGGAGTGGGTGCAGGCTCTGGCCCTCACTTCATGTTAGACTTCTCAGGTTTATATT
 241 TAAGTGTTTTTAAATGGAAAATTGGTGCTACTATTAAATCACACAGTTGAGACATGGGTTTCGAAATTGCTTCGGCCTGA
 321 TGATGCCACTTCTGTTTAAGCGAGGCAGAAGGTCTTTGACAGGCTTCATTTAAACAGAAGCATTTGGCAAATGGAACAGG
 401 ATCTTATAAAATAATATCCTGGGCCAAAATCCCTACAGGGATACTAGGGCTTTCTCCCACTGCTCCCTCATGTCTGCCAT
 481 CTTCCCCTTCAGGGCCCTTCAGCGTCTAATAACAATACCAACACAAACCTGCACCTTGCGACCATGTCCACCCTTCTACA
 561 CAGGACTGTCACATTATCAAGCCACAGTTAGAAATAATCTTGTTTCCACTTAGAAAATGTGTAAATACTGCCTTGCTGTA
 641 AATTGAATGTGAAATCCTTTGGTCCTATGCCATGTTGAGTGACCCGAATAGCCCCTTGCATCGGCAGGATGGTCTGCAGC
 721 CACCACCTGCCTTGGTTCCTGGCCATGGTGTAGGGAGGGTGATGGTCTGCAGCCACCACCTGCCTTGGTTCCTGGCCATG
 801 GTGTAGGGAGGGTGATTCACTCTCCAGGTCCTTTGAATAGGTGACAGACAGGCAGAGCCTGAATGTCAGGAAATTCCATT
 881 GTATGAATGCTTTAAAGGAAAACGTTCCCTATACCTCATTATTTTTTATTGCATGATGTTTTATAAAAATTTGCCCATTT
 961 TAGATGTTAGAAAAATTATTTCCACTATGCAAATTTCTTTTTAATTCAGTGAAAAGCAACTGTTATACCTCATAGTCTCT
1041 TGTTTTTAATTGACCAAAATATTCCATTCTATTCTCACAAGGTTCTGAGGTCTCTGCCTGAAAAAGCAAGTCTCACCCTA
1121 TAGACACTGATGTGCCCAGCACTACGTGCCAGCCATTGTGGGAACACAAGAGGGTCACCTGCCCAAGGGCTAGGGAGGAA
1201 GACCTCAAGAACACAGAGGAGGTGGAAAAGGACAAAATAGGTGCCATTTTAGGGAGACCATGGTCAGATAGGGGGATGCT
1281 CAGTTCCTTGCAGCCTCGGGCGGGCTTATGTTGGCACTAAGGCCATTGTGGAGTGTACTTATATGATCCCTATGCTGATA
1361 GGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTG
1441 TGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAA
1521 GCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGA
1601 AGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCT
1681 GGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCC
1761 AAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGC
1841 AGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCAT
1921 TGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTT
2001 CCTTGTATTCAGTCCATTACCAAAGAGGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCACATCGT
2081 TAAGTGGAAAAAAAAAAAAAAAAAAA
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' ggAGAUCAUUUAUACAGUCGUa 5'
            || |  :|| ||||| ||| 
Target 5' ttTCAAACGAAGATGTCTGCAg 3'
 1821 - 1842 132.00 -7.99
2 
miRNA  3' ggAGAUCAUUU--AUACAGUCGUa 5'
            || :| :::  |||||::||| 
Target 5' ccTCGGGCGGGCTTATGTTGGCAc 3'
 1294 - 1317 126.00 -12.50
3 
miRNA  3' ggaGA-UCAUUUAUACAGUCGUa 5'
             || || |||   | ||||| 
Target 5' ctgCTGAGCAAA---GACAGCAt 3'
 1408 - 1427 120.00 -6.70
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HS5
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP聽 data was present in GSM1013108. RNA binding protein: AGO. Condition:HS5-replicate-3 ...

- Balakrishnan I; Yang X; Brown J; et al., 2014, Stem cells (Dayton, Ohio).

Article - Balakrishnan I; Yang X; Brown J; et al.
- Stem cells (Dayton, Ohio), 2014
Regulation of hematopoietic stem cell proliferation, lineage commitment, and differentiation in adult vertebrates requires extrinsic signals provided by cells in the marrow microenvironment (ME) located within the bone marrow. Both secreted and cell-surface bound factors critical to this regulation have been identified, yet control of their expression by cells within the ME has not been addressed. Herein we hypothesize that microRNAs (miRNAs) contribute to their controlled expression. MiRNAs are small noncoding RNAs that bind to target mRNAs and downregulate gene expression by either initiating mRNA degradation or preventing peptide translation. Testing the role of miRNAs in downregulating gene expression has been difficult since conventional techniques used to define miRNA-mRNA interactions are indirect and have high false-positive and negative rates. In this report, a genome-wide biochemical technique (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation or HITS-CLIP) was used to generate unbiased genome-wide maps of miRNA-mRNA interactions in two critical cellular components of the marrow ME: marrow stromal cells and bone marrow endothelial cells. Analysis of these datasets identified miRNAs as direct regulators of JAG1, WNT5A, MMP2, and VEGFA; four factors that are important to ME function. Our results show the feasibility and utility of unbiased genome-wide biochemical techniques in dissecting the role of miRNAs in regulation of complex tissues such as the marrow ME.
LinkOut: [PMID: 24038734]
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_012293 | 3UTR | UGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
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_012293 | 3UTR | CUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
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_012293 | 3UTR | CCUGGGAACCUCUGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
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_012293 | 3UTR | CUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_012293 | 3UTR | UCUUCCCUGGGAACCUCUGAACUCCUCCUUCCUCUGGGCUCUCUGUAACAUUUCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM1013108
Method / RBP HITS-CLIP  / AGO
Cell line / Condition HS5 / HS5-replicate-3
Location of target site ENST00000252804.4 | 3UTR | UCACCACACGUCAGCAUCUAAUCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24038734 / GSE41272
CLIP-seq Viewer Link
44 hsa-miR-628-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT037783 NELFE negative elongation factor complex member E 1 1
MIRT200944 ZNF264 zinc finger protein 264 2 6
MIRT441916 ACADSB acyl-CoA dehydrogenase, short/branched chain 2 2
MIRT443436 PLSCR1 phospholipid scramblase 1 2 2
MIRT443447 CLIC5 chloride intracellular channel 5 2 2
MIRT443906 ZNF256 zinc finger protein 256 2 2
MIRT449750 SMYD2 SET and MYND domain containing 2 2 2
MIRT461377 SLFN12L schlafen family member 12 like 2 2
MIRT466416 TFAP2A transcription factor AP-2 alpha 2 8
MIRT486594 CTPS2 CTP synthase 2 2 2
MIRT491945 VPS52 VPS52, GARP complex subunit 2 2
MIRT513492 SSR1 signal sequence receptor subunit 1 2 6
MIRT528599 ZNF326 zinc finger protein 326 2 2
MIRT531325 SEMA3D semaphorin 3D 2 2
MIRT532082 RTTN rotatin 2 2
MIRT532563 CSTF1 cleavage stimulation factor subunit 1 2 2
MIRT532976 ZNF12 zinc finger protein 12 2 2
MIRT534075 SREK1IP1 SREK1 interacting protein 1 2 2
MIRT536103 MBNL1 muscleblind like splicing regulator 1 2 4
MIRT536183 MAOB monoamine oxidase B 2 2
MIRT543755 UBXN2B UBX domain protein 2B 2 2
MIRT550000 KIAA0408 KIAA0408 2 2
MIRT551237 COLEC10 collectin subfamily member 10 2 2
MIRT567554 FEN1 flap structure-specific endonuclease 1 2 2
MIRT570387 UBE2D4 ubiquitin conjugating enzyme E2 D4 (putative) 2 2
MIRT570808 LYN LYN proto-oncogene, Src family tyrosine kinase 2 2
MIRT576346 Pxdn peroxidasin 2 2
MIRT576520 Txlna taxilin alpha 2 2
MIRT576893 Poteg POTE ankyrin domain family, member G 2 2
MIRT606796 BICD2 BICD cargo adaptor 2 2 2
MIRT625909 GBP6 guanylate binding protein family member 6 2 2
MIRT626869 PDGFRA platelet derived growth factor receptor alpha 2 2
MIRT643603 IRAK4 interleukin 1 receptor associated kinase 4 2 2
MIRT645451 FOXE1 forkhead box E1 2 2
MIRT652265 TOMM20 translocase of outer mitochondrial membrane 20 2 2
MIRT689023 ARID1A AT-rich interaction domain 1A 2 2
MIRT691057 CRCP CGRP receptor component 2 2
MIRT704712 CHD9 chromodomain helicase DNA binding protein 9 2 2
MIRT713069 ENTHD1 ENTH domain containing 1 2 2
MIRT719483 RBM27 RNA binding motif protein 27 2 2
MIRT732944 AGAP2-AS1 AGAP2 antisense RNA 1 3 0
MIRT732945 KLF12 Kruppel like factor 12 3 0
MIRT733520 BMP2 bone morphogenetic protein 2 3 0
MIRT733521 ETV1 ETS variant 1 3 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-628-5p 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-628 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-628-5p Sunitinib 5329102 NSC750690 approved sensitive Low Renal Cell Cancer tissue
hsa-miR-628-5p Sunitinib 5329102 NSC750690 approved sensitive Low Renal Cell Cancer cell line (OS-RC-2)
hsa-miR-628-5p Trametinib 11707110 NSC758246 approved sensitive High Melanoma cell line
hsa-miR-628-5p Dabrafenib + Trametinib sensitive High Melanoma cell line
hsa-miR-628-5p Dabrafenib 44462760 NSC764134 approved sensitive High Melanoma cell line
hsa-miR-628-5p Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line
hsa-miR-628-5p Vincristine 5978 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-628-5p Vinorelbine 44424639 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-628-5p Doxorubicin 31703 NSC123127 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-628-5p Etoposide 36462 NSC141540 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-628-5p Paclitaxel 36314 NSC125973 approved resistant High Colorectal Cancer cell line (HCT8)
hsa-miR-628-5p Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-628-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-628-5p Osimertinib 71496458 NSC779217 approved resistant cell line (PC9)
hsa-miR-628-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-628-5p Gefitinib 123631 NSC715055 approved sensitive cell line (HCC827)
hsa-miR-628-5p Paclitaxel 36314 NSC125973 approved resistant cell line (SKVO3ip1)
hsa-miR-628-5p Paclitaxel 36314 NSC125973 approved sensitive cell line (HeyA8)
hsa-miR-628-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM43)
hsa-miR-628-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM16)
hsa-miR-628-5p Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM47)
hsa-miR-628-5p Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-miR-628-5p Doxorubicin 31703 NSC123127 approved resistant cell line (BAS)
hsa-miR-628-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-628-5p Ethanol+Tamoxifen sensitive cell line (LY2)
hsa-miR-628-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (RPMI2650)
hsa-miR-628-5p Sunitinib 5329102 NSC750690 approved resistant tissue (CardA)
hsa-miR-628-5p Platinum-based doublet chemotherapy resistant tissue (lung adenocarcinoma)
hsa-miR-628-5p Tamoxifen 2733525 NSC180973 approved sensitive cell line (TamR4)
hsa-miR-628-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-628-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-628-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (H23)
hsa-miR-628-5p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)
hsa-miR-628-5p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide sensitive cell line (Bads-200)

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