pre-miRNA Information
pre-miRNA hsa-mir-1245a   
Genomic Coordinates chr2: 188978092 - 188978161
Description Homo sapiens miR-1245a stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-1245a
Sequence 45| AAGUGAUCUAAAGGCCUACAU |65
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN31562560 15 COSMIC
COSN26581044 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs906938680 2 dbSNP
rs1159117523 3 dbSNP
rs780486044 6 dbSNP
rs771479866 17 dbSNP
rs1002976932 18 dbSNP
rs1428029219 19 dbSNP
Putative Targets

Gene Information
Gene Symbol SEC24D   
Synonyms CLCRP2
Description SEC24 homolog D, COPII coat complex component
Transcript NM_014822   
Expression
Putative miRNA Targets on SEC24D
3'UTR of SEC24D
(miRNA target sites are highlighted)
>SEC24D|NM_014822|3'UTR
   1 TTGAAACTTCTCTGTCATTGATGTTGCATTTCCAAGGAGATAATCTCCTTCTTGGTGCCTAATTTTCTAGATGATAATAG
  81 GCTAGTTTTGATTTCTTGCTCATTTTCAGAATAACTTTCCAGGAAGAGATGGCATTTAGAACTTCAGCTTTGGTGCTCAG
 161 GTATAAAGCCAATTAAGGTACAATTGTACCATAAAGGGAACAATCTGTTTCTGATTGCACAGTTTCTAATTTTTAAAACT
 241 GATGTGGTTTGCATTTCATAAAAGGCAAAGTTTACAGAACCATAAACATTCTCAATTTTCTTTATGCTAGACATATAAAT
 321 TATTTTTCAAACTGTATAGATTTGGGGTAAAAAGTTGTCTCAGTTCCTCTCCCAATTGCAATGAGAAAAAAAAGCTTAAT
 401 TTTTACATTATACTTAATTTTCTAAAACCATGTAACTCCATTGAACACATTTTTCAACTTAAGGTCTGCATAGCAGACTT
 481 TTAATAACCTTGGGATTTATCTGGTAGAACAATATGTGTTCTACATTTTTTTCATAATTATATATTGTGTATGTTAAAAC
 561 TATTTTCCAGTTGTTTTGTCTGTAAAACTGTCTTTATCAATATGCTTAATGGTTCTTTGTACAATTTTGAAAGTTTCTAC
 641 CTGTATATAATGGATGTTAACCAGTATCAATAAATCACTTCGTATAATCTTAAAAAAAAAAAAAAA
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' uaCAUCCGGAAAUCUAGUGAa 5'
            |||  :|  || |||||| 
Target 5' caGTA--TCAATAAATCACTt 3'
662 - 680 123.00 -5.70
2
miRNA  3' uacAUCCGG--AAAUCUAGUGAa 5'
             |||||:  ||| |||: || 
Target 5' taaTAGGCTAGTTTTGATTTCTt 3'
75 - 97 120.00 -8.70
3
miRNA  3' uacaucCGGAAAUCUAGUGAa 5'
                |:||||  |||| | 
Target 5' aaaactGTCTTT--ATCAATa 3'
584 - 602 98.00 -5.02
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
1181948 172 ClinVar
COSN30152377 47 COSMIC
COSN5051480 71 COSMIC
COSN30150847 126 COSMIC
COSN31527335 212 COSMIC
COSN29395316 265 COSMIC
COSN31523924 397 COSMIC
COSN31609148 425 COSMIC
COSN31530561 681 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1486077264 1 dbSNP
rs1186702152 2 dbSNP
rs768293988 3 dbSNP
rs768845637 7 dbSNP
rs747558960 8 dbSNP
rs1425372432 10 dbSNP
rs1165077788 12 dbSNP
rs1193851720 18 dbSNP
rs1407857251 19 dbSNP
rs1399423418 20 dbSNP
rs775824353 25 dbSNP
rs374214917 26 dbSNP
rs1223123144 29 dbSNP
rs745928760 35 dbSNP
rs1311274871 36 dbSNP
rs779170223 37 dbSNP
rs757454816 38 dbSNP
rs749450416 39 dbSNP
rs1279082994 41 dbSNP
rs1489357830 44 dbSNP
rs760263151 45 dbSNP
rs777624625 48 dbSNP
rs755825038 50 dbSNP
rs775267354 50 dbSNP
rs1276753000 51 dbSNP
rs550715370 65 dbSNP
rs1029179283 74 dbSNP
rs1221941902 78 dbSNP
rs1165157135 84 dbSNP
rs1422346828 111 dbSNP
rs1354146658 114 dbSNP
rs187212597 116 dbSNP
rs752205242 118 dbSNP
rs1430839523 119 dbSNP
rs370583638 122 dbSNP
rs1020255967 128 dbSNP
rs1231769944 139 dbSNP
rs563055755 146 dbSNP
rs1186310846 148 dbSNP
rs1488972618 153 dbSNP
rs1010280635 156 dbSNP
rs79586191 172 dbSNP
rs1220604364 183 dbSNP
rs1409429683 184 dbSNP
rs1036041279 190 dbSNP
rs772945797 193 dbSNP
rs1377682455 198 dbSNP
rs905664609 200 dbSNP
rs1435514935 201 dbSNP
rs1328446944 204 dbSNP
rs1048234041 211 dbSNP
rs1056062720 213 dbSNP
rs931028218 215 dbSNP
rs939012823 282 dbSNP
rs1377620436 289 dbSNP
rs886227272 293 dbSNP
rs1277877387 294 dbSNP
rs1358965383 315 dbSNP
rs1271931457 323 dbSNP
rs1275489976 323 dbSNP
rs1229644498 335 dbSNP
rs1309200864 336 dbSNP
rs1239285595 337 dbSNP
rs771838798 342 dbSNP
rs1192328292 345 dbSNP
rs1047454060 357 dbSNP
rs1435729414 359 dbSNP
rs1167555613 375 dbSNP
rs1394682696 378 dbSNP
rs1801879 379 dbSNP
rs1036649593 384 dbSNP
rs930501098 391 dbSNP
rs1329671191 394 dbSNP
rs1393878288 394 dbSNP
rs943733974 408 dbSNP
rs1440017976 412 dbSNP
rs1301176672 422 dbSNP
rs1372825156 428 dbSNP
rs1213916740 430 dbSNP
rs1345976416 436 dbSNP
rs1337083998 441 dbSNP
rs1304710054 445 dbSNP
rs574247912 448 dbSNP
rs145220003 453 dbSNP
rs1212288726 463 dbSNP
rs932264782 466 dbSNP
rs1255514712 469 dbSNP
rs540231026 470 dbSNP
rs974958793 471 dbSNP
rs1476491780 476 dbSNP
rs943270588 478 dbSNP
rs1417183264 500 dbSNP
rs1459945351 504 dbSNP
rs922060918 510 dbSNP
rs978954317 514 dbSNP
rs1317322092 515 dbSNP
rs1324486850 521 dbSNP
rs1229083234 523 dbSNP
rs182872788 525 dbSNP
rs1170438416 532 dbSNP
rs1230990266 534 dbSNP
rs15128 543 dbSNP
rs987506059 545 dbSNP
rs140430151 547 dbSNP
rs1489118290 547 dbSNP
rs956025156 556 dbSNP
rs1260029155 560 dbSNP
rs1032198616 561 dbSNP
rs1481040071 562 dbSNP
rs978857583 566 dbSNP
rs1431960926 576 dbSNP
rs571060983 578 dbSNP
rs1474253791 584 dbSNP
rs1197670102 593 dbSNP
rs764781096 594 dbSNP
rs144149070 596 dbSNP
rs1458301721 596 dbSNP
rs1382424406 600 dbSNP
rs968786826 604 dbSNP
rs1023134408 609 dbSNP
rs191831989 615 dbSNP
rs1354484911 617 dbSNP
rs896103787 618 dbSNP
rs1294552965 619 dbSNP
rs988793641 619 dbSNP
rs1321818002 620 dbSNP
rs1259492836 622 dbSNP
rs146746449 624 dbSNP
rs1452152388 625 dbSNP
rs1217869026 639 dbSNP
rs1203792276 648 dbSNP
rs1257038843 653 dbSNP
rs1035708063 661 dbSNP
rs1324148094 663 dbSNP
rs1190357187 664 dbSNP
rs186928596 670 dbSNP
rs547651736 680 dbSNP
rs149722407 681 dbSNP
rs553245330 682 dbSNP
rs1362047832 687 dbSNP
rs1421269358 692 dbSNP
rs1159075265 693 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
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 GSM1084042. RNA binding protein: AGO2. Condition:CLIP_noarsenite_rep2 HITS-CLIP data was present in GSM1084043. RNA binding protein: AGO2. Condition:CLIP_arsenite_rep2 ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uacaUCCGGAAAUCUAGUGAa 5'
              ||||   |:||||||| 
Target 5' -ccaAGGCAGGUGGAUCACUu 3'
1 - 20
Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084042
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_noarsenite_rep2
Location of target site ENST00000429811.2 | 3UTR | GCAGGUGGAUCACUUGAGGUCAGGAGUUCAAGACCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084043
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_arsenite_rep2
Location of target site ENST00000429811.2 | 3UTR | CCAAGGCAGGUGGAUCACUUGAGGUCAGGAGUUCAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
BLCA -0.965 0.08 -0.500 0.33 3 Click to see details
HNSC 0.576 0.09 0.643 0.06 7 Click to see details
UCEC 0.962 0.09 1.000 0.5 3 Click to see details
BRCA 1 0.5 1.000 0.5 3 Click to see details
BRCA 1 0.5 1.000 0.5 3 Click to see details
BRCA 1 0.5 1.000 0.5 3 Click to see details
BRCA 1 0.5 1.000 0.5 3 Click to see details
BRCA 1 0.5 1.000 0.5 3 Click to see details
109 hsa-miR-1245a Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT006574 BRCA2 BRCA2, DNA repair associated 2 1
MIRT055432 SHOC2 SHOC2, leucine rich repeat scaffold protein 2 2
MIRT063879 RASSF8 Ras association domain family member 8 2 6
MIRT077025 WIPF2 WAS/WASL interacting protein family member 2 2 2
MIRT095775 GRPEL2 GrpE like 2, mitochondrial 2 10
MIRT099172 MAP3K4 mitogen-activated protein kinase kinase kinase 4 2 2
MIRT175616 OCRL OCRL, inositol polyphosphate-5-phosphatase 2 2
MIRT456518 LYPLAL1 lysophospholipase like 1 2 2
MIRT464457 UGCG UDP-glucose ceramide glucosyltransferase 2 2
MIRT465747 TMPPE transmembrane protein with metallophosphoesterase domain 2 2
MIRT468257 SFXN4 sideroflexin 4 2 2
MIRT469216 RICTOR RPTOR independent companion of MTOR complex 2 2 2
MIRT472045 NPAT nuclear protein, coactivator of histone transcription 2 2
MIRT481795 APEX1 apurinic/apyrimidinic endodeoxyribonuclease 1 2 2
MIRT500154 CREBBP CREB binding protein 2 2
MIRT506514 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 2 4
MIRT506915 KBTBD8 kelch repeat and BTB domain containing 8 2 6
MIRT513901 GRB10 growth factor receptor bound protein 10 2 6
MIRT519128 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) 2 2
MIRT528121 FOXH1 forkhead box H1 2 2
MIRT528942 SFMBT2 Scm like with four mbt domains 2 2 2
MIRT540580 CEP89 centrosomal protein 89 2 2
MIRT545858 ZNF264 zinc finger protein 264 2 4
MIRT547147 PGM3 phosphoglucomutase 3 2 2
MIRT547434 MED4 mediator complex subunit 4 2 2
MIRT554650 ROBO1 roundabout guidance receptor 1 2 2
MIRT558524 CSRNP3 cysteine and serine rich nuclear protein 3 2 2
MIRT559762 ABHD5 abhydrolase domain containing 5 2 2
MIRT560438 GOLGA7B golgin A7 family member B 2 2
MIRT561974 LRRC59 leucine rich repeat containing 59 2 2
MIRT562442 DDIT4 DNA damage inducible transcript 4 2 2
MIRT563489 ZWINT ZW10 interacting kinetochore protein 2 2
MIRT568265 BMP2K BMP2 inducible kinase 2 2
MIRT572522 KIAA0232 KIAA0232 2 2
MIRT612801 LSM14A LSM14A, mRNA processing body assembly factor 2 2
MIRT621533 ZNF507 zinc finger protein 507 2 2
MIRT625205 GSTCD glutathione S-transferase C-terminal domain containing 2 2
MIRT625615 ZNF84 zinc finger protein 84 2 2
MIRT629215 C12orf66 chromosome 12 open reading frame 66 2 2
MIRT629509 AS3MT arsenite methyltransferase 2 2
MIRT629769 STK25 serine/threonine kinase 25 2 2
MIRT630908 GATAD1 GATA zinc finger domain containing 1 2 2
MIRT632508 RAB13 RAB13, member RAS oncogene family 2 2
MIRT636871 ARSE arylsulfatase E (chondrodysplasia punctata 1) 2 2
MIRT637106 CXorf23 BCLAF1 and THRAP3 family member 3 2 2
MIRT637332 FAM9B family with sequence similarity 9 member B 2 2
MIRT637553 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT637639 ZNF431 zinc finger protein 431 2 2
MIRT637836 CACNG8 calcium voltage-gated channel auxiliary subunit gamma 8 2 2
MIRT638326 RNF11 ring finger protein 11 2 2
MIRT638393 RAB11FIP1 RAB11 family interacting protein 1 2 2
MIRT642450 CLUAP1 clusterin associated protein 1 2 2
MIRT642616 APOPT1 apoptogenic 1, mitochondrial 2 2
MIRT643133 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT644324 NFKBID NFKB inhibitor delta 2 2
MIRT645150 DIS3 DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease 2 2
MIRT645673 ADK adenosine kinase 2 2
MIRT646091 MGST3 microsomal glutathione S-transferase 3 2 2
MIRT646858 SLC35E4 solute carrier family 35 member E4 2 2
MIRT650153 ZNF426 zinc finger protein 426 2 2
MIRT652483 TMEM181 transmembrane protein 181 2 2
MIRT653790 SIRPA signal regulatory protein alpha 2 2
MIRT655526 PAG1 phosphoprotein membrane anchor with glycosphingolipid microdomains 1 2 2
MIRT657077 JPH2 junctophilin 2 2 2
MIRT657322 HOOK3 hook microtubule tethering protein 3 2 2
MIRT662036 FUT2 fucosyltransferase 2 2 2
MIRT662322 ADM2 adrenomedullin 2 2 2
MIRT663211 DARS2 aspartyl-tRNA synthetase 2, mitochondrial 2 2
MIRT663559 CCR6 C-C motif chemokine receptor 6 2 2
MIRT663937 ZNF554 zinc finger protein 554 2 2
MIRT664689 EIF2B2 eukaryotic translation initiation factor 2B subunit beta 2 2
MIRT664709 PAICS phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase 2 2
MIRT665291 ZFP14 ZFP14 zinc finger protein 2 2
MIRT665572 TXNL1 thioredoxin like 1 2 2
MIRT667068 PAOX polyamine oxidase 2 2
MIRT667304 MYO5A myosin VA 2 2
MIRT667442 METTL14 methyltransferase like 14 2 2
MIRT668048 GTPBP10 GTP binding protein 10 2 2
MIRT669604 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT671088 ABL2 ABL proto-oncogene 2, non-receptor tyrosine kinase 2 2
MIRT674361 SLC35E3 solute carrier family 35 member E3 2 2
MIRT674962 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT676394 SEC24D SEC24 homolog D, COPII coat complex component 2 2
MIRT676819 AGMAT agmatinase 2 2
MIRT676891 ENSA endosulfine alpha 2 2
MIRT677059 ZNF34 zinc finger protein 34 2 2
MIRT678424 ANKRD36 ankyrin repeat domain 36 2 2
MIRT678735 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT678930 XPOT exportin for tRNA 2 2
MIRT678954 MYADM myeloid associated differentiation marker 2 2
MIRT679228 MAN2A2 mannosidase alpha class 2A member 2 2 2
MIRT679765 TLR6 toll like receptor 6 2 2
MIRT681992 HRH4 histamine receptor H4 2 2
MIRT687405 NSUN4 NOP2/Sun RNA methyltransferase family member 4 2 2
MIRT694570 RBMXL1 RNA binding motif protein, X-linked like 1 2 2
MIRT698449 TM4SF1 transmembrane 4 L six family member 1 2 2
MIRT706406 HAS2 hyaluronan synthase 2 2 2
MIRT706582 ZNF432 zinc finger protein 432 2 2
MIRT706838 VHLL VHL like 2 2
MIRT706909 DVL3 dishevelled segment polarity protein 3 2 2
MIRT707052 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT708583 C11orf54 chromosome 11 open reading frame 54 2 2
MIRT708988 CABP4 calcium binding protein 4 2 2
MIRT713041 ADRA2B adrenoceptor alpha 2B 2 2
MIRT713731 SUCO SUN domain containing ossification factor 2 2
MIRT714968 RAB21 RAB21, member RAS oncogene family 2 2
MIRT717485 PDE4DIP phosphodiesterase 4D interacting protein 2 2
MIRT722826 KLK2 kallikrein related peptidase 2 2 2
MIRT723305 MOGAT1 monoacylglycerol O-acyltransferase 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-1245a Trametinib 11707110 NSC758246 approved resistant High Melanoma cell line (M14) (500nM)
hsa-miR-1245a Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (M14) (500nM)
hsa-miR-1245a Trametinib 11707110 NSC758246 approved resistant High Melanoma cell line (M14) (1uM)
hsa-miR-1245a Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (M14) (1uM)
hsa-miR-1245a Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-1245a Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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