miRTarBase - #MIRT576360


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pre-miRNA Information
pre-miRNA hsa-mir-635   
Genomic Coordinates chr17: 68424451 - 68424548
Synonyms MIRN635, hsa-mir-635, MIR635
Description Homo sapiens miR-635 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-635
Sequence 16| ACUUGGGCACUGAAACAAUGUCC |38
Evidence Experimental
Experiments SAGE
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30524107 5 COSMIC
COSN492359 18 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1431386008 2 dbSNP
rs1200120170 6 dbSNP
rs1477452388 8 dbSNP
rs765045345 10 dbSNP
rs761495041 14 dbSNP
rs1447802278 18 dbSNP
rs994692593 18 dbSNP
rs776535164 23 dbSNP
Putative Targets

Biomarker Information
Biomarker ID Name Type Discovered From Mode Level Source Testing Methods
B0Q4NY miR-635 Predictive Biomarker (PRD) Transcriptomic Data . . . .
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' ccuguaacaaAGU-CACGGGUUCa 5'
                    |||  |||||||| 
Target 5' cacaagagggTCACCTGCCCAAGg 3'
 1165 - 1188 149.00 -13.60
2 
miRNA  3' ccUGUAA---CAAAGUCACGGGUUCa 5'
            |::||   |  ||| ||||||:| 
Target 5' tgATGTTACAGCCTCATTGCCCAGGc 3'
 1853 - 1878 145.00 -15.60
3 
miRNA  3' ccUGUAAC--AAAGU---CACGGGUUCa 5'
            || | |  |||||   | |||||:| 
Target 5' gtACCTGGCATTTCACATGAGCCCAGGg 3'
 1683 - 1710 143.00 -14.80
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 GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_012293 | 3UTR | CCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 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 3 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 4 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 5 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 6 for dataset GSM4903837
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_b
Location of target site NM_012293 | 3UTR | UCCCAAGACAAACAUUCCCGCUGCUCGAAGCAGCUGUAUAGCCUGUGACUCUCCGU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 7 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 8 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
48 hsa-miR-635 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT055249 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT150167 MIDN midnolin 2 2
MIRT198486 USP14 ubiquitin specific peptidase 14 2 6
MIRT446204 GTPBP4 GTP binding protein 4 2 2
MIRT453083 SUMF2 sulfatase modifying factor 2 2 6
MIRT462505 MTFMT mitochondrial methionyl-tRNA formyltransferase 2 8
MIRT474413 KLHL28 kelch like family member 28 2 8
MIRT479376 CELF1 CUGBP Elav-like family member 1 2 4
MIRT498090 SEMA7A semaphorin 7A (John Milton Hagen blood group) 2 2
MIRT525565 MTRNR2L7 MT-RNR2-like 7 2 6
MIRT525613 MTRNR2L3 MT-RNR2-like 3 2 4
MIRT531868 POF1B premature ovarian failure, 1B 2 2
MIRT535789 MTRNR2L11 MT-RNR2-like 11 2 6
MIRT535807 MTRNR2L10 MT-RNR2-like 10 2 4
MIRT539940 IFNAR2 interferon alpha and beta receptor subunit 2 2 2
MIRT563194 C15orf38-AP3S2 C15orf38-AP3S2 readthrough 2 2
MIRT563803 AP3S2 adaptor related protein complex 3 sigma 2 subunit 2 2
MIRT576360 Pxdn peroxidasin 2 2
MIRT615575 NCS1 neuronal calcium sensor 1 2 2
MIRT620858 SERPING1 serpin family G member 1 2 2
MIRT623189 NAA15 N(alpha)-acetyltransferase 15, NatA auxiliary subunit 2 2
MIRT625116 SLC1A5 solute carrier family 1 member 5 2 2
MIRT625128 NUP93 nucleoporin 93 2 2
MIRT625904 LINC00632 long intergenic non-protein coding RNA 632 2 2
MIRT626820 PRR11 proline rich 11 2 2
MIRT628142 HM13 histocompatibility minor 13 2 2
MIRT633789 ZNF490 zinc finger protein 490 2 2
MIRT634385 RAP2B RAP2B, member of RAS oncogene family 2 2
MIRT636563 EPB41 erythrocyte membrane protein band 4.1 2 2
MIRT643446 LAX1 lymphocyte transmembrane adaptor 1 2 2
MIRT646006 HTRA1 HtrA serine peptidase 1 2 2
MIRT652141 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652672 TIMELESS timeless circadian clock 2 2
MIRT658341 FAM83D family with sequence similarity 83 member D 2 2
MIRT658890 DRAXIN dorsal inhibitory axon guidance protein 2 2
MIRT659518 CHST3 carbohydrate sulfotransferase 3 2 2
MIRT668590 ELAVL3 ELAV like RNA binding protein 3 2 2
MIRT670258 ZKSCAN3 zinc finger with KRAB and SCAN domains 3 2 2
MIRT686721 TBC1D13 TBC1 domain family member 13 2 2
MIRT701899 MNT MAX network transcriptional repressor 2 2
MIRT702764 IGF1R insulin like growth factor 1 receptor 2 2
MIRT705290 B4GALT1 beta-1,4-galactosyltransferase 1 2 2
MIRT710836 BASP1 brain abundant membrane attached signal protein 1 2 2
MIRT711732 NUPL2 nucleoporin like 2 2 2
MIRT717619 SLC30A10 solute carrier family 30 member 10 2 2
MIRT719453 APBA1 amyloid beta precursor protein binding family A member 1 2 2
MIRT720819 CIAO1 cytosolic iron-sulfur assembly component 1 2 2
MIRT723454 CUL4A cullin 4A 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-635 Doxorubicin 31703 NSC123127 approved sensitive High Hepatocellular Carcinoma tissue and cell line (HepG2)
hsa-miR-635 Cisplatin 5460033 NSC119875 approved resistant cell line
hsa-miR-635 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM36)
hsa-miR-635 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM11)
hsa-miR-635 Vemurafenib 42611257 NSC761431 approved sensitive cell line (LM47)
hsa-miR-635 Paclitaxel 36314 NSC125973 approved resistant cell line (PC3PR200)
hsa-miR-635 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-635 Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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