pre-miRNA Information | |
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pre-miRNA | hsa-mir-6509 |
Genomic Coordinates | chr7: 135206994 - 135207078 |
Description | Homo sapiens miR-6509 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-6509-3p | |||||||||||||||||||||||||||||||||
Sequence | 52| UUCCACUGCCACUACCUAAUUU |73 | |||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TIMM10B | ||||||||||||||||||||
Synonyms | FXC1, TIM10B, Tim9b | ||||||||||||||||||||
Description | translocase of inner mitochondrial membrane 10B | ||||||||||||||||||||
Transcript | NM_012192 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TIMM10B | |||||||||||||||||||||
3'UTR of TIMM10B (miRNA target sites are highlighted) |
>TIMM10B|NM_012192|3'UTR 1 CCATACCCAACCCCAGGAAGGAAGGCCTTGGATGGACCCTCAGATTGAAGGACCCGGTGGACCTTGGGGTTGGTGAATCC 81 TAAACAGAGAGAATTCGAGGTTGCCTGAAAGCTGGGTGTCCTTGCTCCTTTTCCTGGAGCCAATATACCCAGTTTTTACT 161 CAGTTTGATTTATATTCTGGGCAAGGAAGCTTTGCCTACTTTATTGGCACAATCCGTTGTTCTGTCGTTTAGTGCATATC 241 TGCTGGCTTCAGCCCTGGCAGCTGAGAAATTGTTTTCTATATGTAGAAGGAAAACCTGAGCATTTGCAGGCATCTGGTTA 321 AAGCAGGGTCTGTGTGTACAATTTTAAAACGGGTAATATGTCATGCTCTTAGTTCATCTTCACAACAAAACTATGAGTAA 401 GCGGTATTAGCCTCACTTAACAGATGAGGAAGCAAGATTCCAGAAAGTACCAGAAGGTCATTTTATACAACAGGAGATTG 481 GTTCCTGCCCAGATGACAGAAAATGGGAGCTCTGTCTAGTTGTCCTTAAGTCTGACTGACTTCAGTGGCTCATAACCGTG 561 AGCCAAGTATTTGTTGGTTCATAACTGTTGTTTTGTGAACTATGTCTTACATGTCTAGAGTTCTGCTGGATCTAGGGAAA 641 GGAGGAGCTATCGAAGTACAACGGATCAAAAAACCACAGGGCTTTTGGGCACTGCCTCCTTGGGAAGTTAGTGGCCACAG 721 AAGAGAGATGAAACCTGTAAGAAGTCTGGAGTCTTTTGGAACTTCAGCCATTTCCCCAGGTTGTTACTTTCTTAGTATGT 801 ACAGTCTTCTCAGGATGAGCAGTAAAACCTTTGAACAAAGGTCTGTGTGGTTGTCTTCACGGGCAATCAGGAAGGGAGAG 881 AGCTGGGGACCATATTCTGCAATGCAGCCAAATCCGAGGAAGAGAAACTGAAGGGAGAAGTAGATGGCAATGGTTATGAT 961 AAAAAGGGATAAAACTAAATCTTCGGGACTTCTTTAATGCTACGTTAATGTTTCACTGCTCGTCTAGAAACTCCTAAATC 1041 CAGCTTTCTATCATCTGCCCCACATTGGTCCCATTGAGTACATTCTGTGATTTCTAATTCCAGCCTCTCCATTCTTTTCT 1121 CATTATTGCCTCCCCCGCCCCCCAACTTTGTGTAATTTACTTCTGTATTCAGCAGCCTGGATAGCATATCATTCCATCAC 1201 CCCATTTTCTTGCCACCATTGGCCATCTTTTTGTATCATTCCACTTATTCTGTCTTTTCCATTCCTTCATTCAAACTGCT 1281 AGAGAAAAACAGTTGTGTAATGAATGCCACTAAATATTCAAGGCCTCCAACCTCAGCCAAGTCCTCACACCAACACGCAG 1361 TCACACCAACACACACCTTTATGGGTTCCTGGTCCATTTCCTTCTCTAATTACCATGGCAGTTATTTTACACCTCTACTG 1441 CTGTCCTTAATCCCATACCCCACCCTCATCAGGTGACCCTGTTTCCTTTTTTAGAGAAATTGAAGCTCTTAGACATTGGT 1521 TTCCACAGTAATAATTTTAAAACTTCTTACAACTACCTACAAAGCAGATGTTCTATCCTATCTACAGAGCAGAAAATTGA 1601 AATTCTCAAGTAGCAGACCCGGTATTAAAGTGCAGATCTGACTTTAAAGTCCATGTTCATTTTACACAGCAGGCTGCCTC 1681 TTAAGATAGTATTTATTGAGCACACACTTTGTGTAGGTTCTGATTTTGGTAGATGTCATGCTTTATATTAATCTTTACAA 1761 CAACTATAAGTAAGAGGTATTAACCTCACTTAACAGATGAGGAAGCAAGAATCCAGAATGTGCCAGAAGGCACATTCTGC 1841 AGATTTCGTGCAAACATTTATACACAGCTTCTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCACCCAGGCTGGAGT 1921 GCAGTGGAGCGATCTAGGCTCACTGCAACCTCCGCCACCCGGGTTCAAGCAGTTCTCCTGCCTCAGCCTCTCGAGTAGCT 2001 GGGATTACAGGCATGCGCCACCACGCCCAGCTAATTTTGTTTTTGTATTTTAAGTAGAGACGGGGTTTCACTGTATTGGT 2081 CAGGCTGGTCTTGAACTCCTGACCTTGTGATCCGCCCGCCTCGGCCTCCAAAAGTGCTGGGATTACAGGTGTGAGCCACC 2161 ACGGCCGGCCTATACAAAGTTTCTTATTGAGAAAAGTGGTTCCAATCATGTTTTTTGCCCCCTTTAGCTGCTATCTCTTG 2241 AACAGAAAAGTTTGTTAGGAAGGTAAAAGTTGCTGACTAGGACCTTACCCACAGGGTGGCACTCTGTCCTTGGGAAATAT 2321 AAATGCAAGTAAAACAGGTTTGAACTTCTTAACTTCCAGAAGATAGGAGGATGGGACCTGTGATACTGTGCTGCTGGTGG 2401 GAGGACCCTTCCACATCAACATTTGTGTGTATCCTTGCAATAAACTTCCATTGTGAATTAAAAAAAAAAAAAAAAAAAA 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 GSM1067869. RNA binding protein: AGO2. Condition:Ago2 IP-seq (asynchronous 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 GSM1067869 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293/HeLa / Ago2 IP-seq (asynchronous cells) |
Location of target site | ENST00000254616.6 | 3UTR | CCAGGCUGGAGUGCAGUGGA |
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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82 hsa-miR-6509-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT055374 | PDCD4 | programmed cell death 4 | ![]() |
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2 | 4 | ||||||
MIRT378341 | MARCKS | myristoylated alanine rich protein kinase C substrate | ![]() |
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2 | 2 | ||||||
MIRT444668 | CDKL2 | cyclin dependent kinase like 2 | ![]() |
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2 | 2 | ||||||
MIRT446953 | CD248 | CD248 molecule | ![]() |
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2 | 2 | ||||||
MIRT460332 | CAMK4 | calcium/calmodulin dependent protein kinase IV | ![]() |
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2 | 6 | ||||||
MIRT464078 | VPS4A | vacuolar protein sorting 4 homolog A | ![]() |
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2 | 2 | ||||||
MIRT464586 | UBN2 | ubinuclein 2 | ![]() |
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2 | 2 | ||||||
MIRT468482 | SESN3 | sestrin 3 | ![]() |
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2 | 2 | ||||||
MIRT468962 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT475455 | HSPA8 | heat shock protein family A (Hsp70) member 8 | ![]() |
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2 | 2 | ||||||
MIRT482403 | ADRB1 | adrenoceptor beta 1 | ![]() |
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2 | 10 | ||||||
MIRT486992 | ZFAND2B | zinc finger AN1-type containing 2B | ![]() |
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2 | 2 | ||||||
MIRT489397 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT526319 | UGT2A1 | UDP glucuronosyltransferase family 2 member A1 complex locus | ![]() |
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2 | 2 | ||||||
MIRT526560 | UGT2A2 | UDP glucuronosyltransferase family 2 member A2 | ![]() |
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2 | 2 | ||||||
MIRT526732 | ZNF138 | zinc finger protein 138 | ![]() |
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2 | 8 | ||||||
MIRT531581 | STXBP5L | syntaxin binding protein 5 like | ![]() |
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2 | 2 | ||||||
MIRT532011 | NOX5 | NADPH oxidase 5 | ![]() |
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2 | 2 | ||||||
MIRT533407 | TXLNG | taxilin gamma | ![]() |
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2 | 2 | ||||||
MIRT533436 | TRPC5 | transient receptor potential cation channel subfamily C member 5 | ![]() |
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2 | 2 | ||||||
MIRT533866 | TBL1XR1 | transducin beta like 1 X-linked receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT539254 | ANKRD50 | ankyrin repeat domain 50 | ![]() |
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2 | 2 | ||||||
MIRT541451 | C15orf48 | chromosome 15 open reading frame 48 | ![]() |
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2 | 2 | ||||||
MIRT566794 | MIER3 | MIER family member 3 | ![]() |
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2 | 2 | ||||||
MIRT569294 | SURF6 | surfeit 6 | ![]() |
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2 | 2 | ||||||
MIRT571336 | RABGEF1 | RAB guanine nucleotide exchange factor 1 | ![]() |
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2 | 2 | ||||||
MIRT572802 | PPP3CB | protein phosphatase 3 catalytic subunit beta | ![]() |
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2 | 2 | ||||||
MIRT572813 | MYO1C | myosin IC | ![]() |
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2 | 2 | ||||||
MIRT574219 | DMRT2 | doublesex and mab-3 related transcription factor 2 | ![]() |
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2 | 2 | ||||||
MIRT607259 | GRAMD1B | GRAM domain containing 1B | ![]() |
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2 | 4 | ||||||
MIRT609307 | CHD4 | chromodomain helicase DNA binding protein 4 | ![]() |
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2 | 2 | ||||||
MIRT615459 | REPS1 | RALBP1 associated Eps domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT616861 | RPLP1 | ribosomal protein lateral stalk subunit P1 | ![]() |
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2 | 2 | ||||||
MIRT619415 | NOS1AP | nitric oxide synthase 1 adaptor protein | ![]() |
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2 | 2 | ||||||
MIRT619652 | COX19 | COX19, cytochrome c oxidase assembly factor | ![]() |
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2 | 2 | ||||||
MIRT625325 | TNFRSF13B | TNF receptor superfamily member 13B | ![]() |
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2 | 2 | ||||||
MIRT638980 | ARFIP2 | ADP ribosylation factor interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT639458 | ZNF429 | zinc finger protein 429 | ![]() |
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2 | 2 | ||||||
MIRT640550 | SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | ![]() |
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2 | 2 | ||||||
MIRT641473 | B4GALNT3 | beta-1,4-N-acetyl-galactosaminyltransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT642720 | ATXN3 | ataxin 3 | ![]() |
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2 | 2 | ||||||
MIRT643048 | SMN1 | survival of motor neuron 1, telomeric | ![]() |
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2 | 2 | ||||||
MIRT644921 | SMN2 | survival of motor neuron 2, centromeric | ![]() |
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2 | 2 | ||||||
MIRT645875 | ZNF275 | zinc finger protein 275 | ![]() |
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2 | 2 | ||||||
MIRT649824 | LIPG | lipase G, endothelial type | ![]() |
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2 | 2 | ||||||
MIRT649851 | GYS2 | glycogen synthase 2 | ![]() |
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2 | 2 | ||||||
MIRT649972 | TRAFD1 | TRAF-type zinc finger domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT650675 | ZNF259 | ZPR1 zinc finger | ![]() |
1 | 1 | |||||||
MIRT651319 | ZCCHC2 | zinc finger CCHC-type containing 2 | ![]() |
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2 | 2 | ||||||
MIRT652876 | TAB1 | TGF-beta activated kinase 1 (MAP3K7) binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT652881 | SYVN1 | synoviolin 1 | ![]() |
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2 | 2 | ||||||
MIRT654144 | RPAP2 | RNA polymerase II associated protein 2 | ![]() |
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2 | 2 | ||||||
MIRT657080 | JMY | junction mediating and regulatory protein, p53 cofactor | ![]() |
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2 | 2 | ||||||
MIRT657181 | INO80C | INO80 complex subunit C | ![]() |
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2 | 2 | ||||||
MIRT657830 | GJD3 | gap junction protein delta 3 | ![]() |
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2 | 2 | ||||||
MIRT657897 | GDF7 | growth differentiation factor 7 | ![]() |
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2 | 2 | ||||||
MIRT659631 | CDKN2AIP | CDKN2A interacting protein | ![]() |
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2 | 2 | ||||||
MIRT663115 | SPTA1 | spectrin alpha, erythrocytic 1 | ![]() |
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2 | 2 | ||||||
MIRT664739 | METTL16 | methyltransferase like 16 | ![]() |
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2 | 2 | ||||||
MIRT667551 | LRAT | lecithin retinol acyltransferase | ![]() |
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2 | 2 | ||||||
MIRT668552 | ERCC1 | ERCC excision repair 1, endonuclease non-catalytic subunit | ![]() |
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2 | 2 | ||||||
MIRT682893 | XIAP | X-linked inhibitor of apoptosis | ![]() |
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2 | 2 | ||||||
MIRT683092 | PRRG4 | proline rich and Gla domain 4 | ![]() |
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2 | 2 | ||||||
MIRT683102 | TIMM10B | translocase of inner mitochondrial membrane 10B | ![]() |
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2 | 2 | ||||||
MIRT697648 | WNK1 | WNK lysine deficient protein kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT709158 | ZNF419 | zinc finger protein 419 | ![]() |
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2 | 2 | ||||||
MIRT713220 | RCAN2 | regulator of calcineurin 2 | ![]() |
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2 | 2 | ||||||
MIRT713277 | LAIR1 | leukocyte associated immunoglobulin like receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT715008 | CYP1B1 | cytochrome P450 family 1 subfamily B member 1 | ![]() |
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2 | 2 | ||||||
MIRT715051 | SYNJ2BP | synaptojanin 2 binding protein | ![]() |
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2 | 2 | ||||||
MIRT715696 | PNMAL2 | paraneoplastic Ma antigen family member 8B | ![]() |
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2 | 2 | ||||||
MIRT717250 | TMEM246 | transmembrane protein 246 | ![]() |
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2 | 2 | ||||||
MIRT717322 | PGK1 | phosphoglycerate kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT717587 | MTHFD1L | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like | ![]() |
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2 | 2 | ||||||
MIRT718122 | CHST4 | carbohydrate sulfotransferase 4 | ![]() |
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2 | 2 | ||||||
MIRT718418 | CALN1 | calneuron 1 | ![]() |
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2 | 2 | ||||||
MIRT718750 | ZNF490 | zinc finger protein 490 | ![]() |
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2 | 2 | ||||||
MIRT720048 | PPP1R3F | protein phosphatase 1 regulatory subunit 3F | ![]() |
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2 | 2 | ||||||
MIRT721497 | THRB | thyroid hormone receptor beta | ![]() |
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2 | 2 | ||||||
MIRT722531 | EPRS | glutamyl-prolyl-tRNA synthetase | ![]() |
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2 | 2 | ||||||
MIRT723279 | KRTAP21-2 | keratin associated protein 21-2 | ![]() |
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2 | 2 | ||||||
MIRT724813 | MSX2 | msh homeobox 2 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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