pre-miRNA Information | |
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pre-miRNA | hsa-mir-8066 |
Genomic Coordinates | chr4: 101240795 - 101240872 |
Description | Homo sapiens miR-8066 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-8066 | |||||||||||||||||||||||||||
Sequence | 48| CAAUGUGAUCUUUUGGAUGUA |68 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | MTMR4 | ||||||||||||||||||||
Synonyms | FYVE-DSP2, ZFYVE11 | ||||||||||||||||||||
Description | myotubularin related protein 4 | ||||||||||||||||||||
Transcript | NM_004687 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on MTMR4 | |||||||||||||||||||||
3'UTR of MTMR4 (miRNA target sites are highlighted) |
>MTMR4|NM_004687|3'UTR 1 ATGCCGGGGAGAAACCTGTCCAATTTTAGCAGGTTTGAAGGGAGGATCTTCTTCAGTTGTAGTTTGGAAGGTTCCTTGGT 81 GTGGCTCATGAAATCACAGAGCTCAGAGATACCATCTTGAGAAATCCTCCTTGGTATCATGAAACTGGAGCAGAGGAATT 161 GCAATTTAGCAGGAGGTCCTCTACTGGTGATACCCTCACCTTGGGGTAATGGTCCTAACCCAGACCCAGGGTCTGGAAGC 241 TTAATGTTGAGTTGGTGACTCCAGCCTCTTTCTCCTGGAGGTCACAAGATGATGATTGCGTAGATGTTGCCTGGTGCAAA 321 GTGCCCCAAACAGCAATAGAAAGGCATATGTATAACCAAACTCCAAGTGATAACCAGACCCATCTCTCCTCCACCTTGAC 401 AAAAGCAGATTATAGTATACAAGGTAGGAATTCCTGTCCTATTTGAGATGAACTATATCCTGTACCTCTGTGCTCTGTGT 481 CTGCATGAAGGCTCAGCCTTTAGAGGCACTCCTTCTAGTTGCATTAGTACTGTCTTTCTGTGGAGTTTGGTTTGAAGACT 561 GGCTCAGCAAGTGGAGGTTTCAATGTATTTTTCAGTTGGCTCATCAGCCAGCATTGGTGAATATTCAGTTTAGGGGAACA 641 GTTCTAGGGAGTGAGACATTTTTGGGAGCAGAGGAAAACTCTGCTGATGTTCGGTCCTGGCAAACATTGAGTTATTTTGA 721 GCTGTGAAGGCAGTCGTCTCTGTTACACAGTGGCAGCTCTTGAGTTATGCACTGTGAAGAATGAGAAGGGAAAAGCAAAA 801 ATTATCCTTGTGAAATATCTGCTGATTGTGCCCTACTCTTTGCACCTGACTTTTCCTAGTTGTCCTGGTGCTAACACAGG 881 AGCTACACCTTGATCCTCTCCTGGCATGAAAATAAAACAAAGGTTTTCGTTGTTGTTGTTCCATTGCCCATTTCCCCCAT 961 GTTGTCTTTCCCTTGGCTGATGCCTCCTCTGGGTCACATTGCTTCTTATCCTGAACACTTGACACCTTGAGGGTAGAATT 1041 TAGCGTTTGGTTTTTACCTCCTAGCATATGCTGTTTGGTATGTGAGGGTTTCAGTACAAATGCTGCTGTCTATTTCTGTG 1121 CACTTAACAATGGAACCCAAACAGAAGAGAATAAAGCCTTGATACCAAAATTGGGAAAGAACATGTGTCCATTTGGACCA 1201 AACGTTGTTGGTTTTTAAAAAATTTTATTTTGTTTTTTTGTTTTTGTTTTTGTTTTTTTTCATCTTAATATGTACCAGTG 1281 GCACTTAACCAAAAGATACAGTGATATAGCCATGTACTGTGGGTGGGACAGATACAGTCTCCTTGGCCTATAATGAAACC 1361 ACTAGGACTTTATACAGTTTTCCTTAATTTGTTGACATATAAATGGTAAATTATATTTAGGCTTATCCTGTTTTGAAATG 1441 ATGGTAGTCATCTTTCTTACTGCTACTTTCATGTTGCTTTCTAGAAAACAGCATTTCATTCCAAAATAACTAGGATCTGC 1521 ATTTAGAACAAGAATCATTATTTGTCCTGACCTTTTCAGTCCTACAGAGACGCATCTGTGGTTCTTTTGTACTTGCCATA 1601 GATGTAACCTAAAAAGTTTTGGCATATTTAGGTCAGCCTAGCGGAACTTTTTTTTTCATTTAAATGGAGCTGAATAATGG 1681 AGATTTTGTGTCTGCAAAATTCCTGAGATCATTGAAAAAGTAACAAGCTGTTCCTTGTTTCTGATACATAAAATTATTTT 1761 AAGCATTTTATCAATCATTAAAATTTACTGCCAGTTGTGAGTGGCTTTTTAATTAACTTGTCTTTCATTGCACTTCACTC 1841 TGCCTGTTTTCAAGGGGAGTAAGATTGGTAACATTTGGGGAGACTGTATCTGTCTACTTAGCGTGGCTGTTTTGAGGGAC 1921 TGTCCCATCAGTGAACAAACTGCATGGCCTTGGAGAGAGACTCTGGGCTCTTGGCTCAGATGTGTTCATCAAATACTCCT 2001 TTCAGAGCTGTTGTGGGTGTAAGTGACATGATGTGGCCAAAAATCCAAACTGTGCAGTTGCGTTGTGACAAACATGCAAT 2081 GTGCTGTAAAAATTCAATACAGTTTAAATAAAATCTCTATATTAGTGCTGCAAAAAAAAAAAAAAAAAA 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 | |||||||||
Disease | 9110.0 | |||||||||
Location of target site | 3'UTR | |||||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | |||||||||
Original Description (Extracted from the article) |
...
"PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | TZM-bl |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
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Experimental Support 3 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | HCT116 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in ERX177634. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_12
... - Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research. |
Article |
- Krell J; Stebbing J; Carissimi C; Dabrowska et al. - Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
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CLIP-seq Support 1 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000579925.1 | 3UTR | UCACAUUGCUUCUUAUCCUGAACACUUGACACCUUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1462574 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | TZM-bl / TZM-bl ami BaL |
Location of target site | ENST00000579925.1 | 3UTR | UCACAUUGCUUCUUAUCCUGAACACUUGACACCUUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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92 hsa-miR-8066 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT060588 | CCND1 | cyclin D1 | ![]() |
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2 | 2 | ||||||
MIRT067440 | RIMKLB | ribosomal modification protein rimK like family member B | ![]() |
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2 | 2 | ||||||
MIRT078862 | WBP2 | WW domain binding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT088062 | UBXN2A | UBX domain protein 2A | ![]() |
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2 | 4 | ||||||
MIRT088214 | NUP50 | nucleoporin 50 | ![]() |
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2 | 2 | ||||||
MIRT103494 | HOXA3 | homeobox A3 | ![]() |
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2 | 8 | ||||||
MIRT135196 | TMBIM6 | transmembrane BAX inhibitor motif containing 6 | ![]() |
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2 | 4 | ||||||
MIRT177727 | REEP3 | receptor accessory protein 3 | ![]() |
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2 | 2 | ||||||
MIRT179439 | TBRG1 | transforming growth factor beta regulator 1 | ![]() |
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2 | 4 | ||||||
MIRT191647 | SLC39A9 | solute carrier family 39 member 9 | ![]() |
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2 | 2 | ||||||
MIRT192342 | KLF13 | Kruppel like factor 13 | ![]() |
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2 | 2 | ||||||
MIRT212035 | RAPGEF2 | Rap guanine nucleotide exchange factor 2 | ![]() |
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2 | 2 | ||||||
MIRT215387 | CREBRF | CREB3 regulatory factor | ![]() |
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2 | 2 | ||||||
MIRT235001 | IER2 | immediate early response 2 | ![]() |
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2 | 2 | ||||||
MIRT238793 | TPD52L1 | tumor protein D52 like 1 | ![]() |
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2 | 2 | ||||||
MIRT273384 | SMARCD1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | ![]() |
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2 | 4 | ||||||
MIRT280473 | UBR7 | ubiquitin protein ligase E3 component n-recognin 7 (putative) | ![]() |
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2 | 2 | ||||||
MIRT298320 | SLC5A3 | solute carrier family 5 member 3 | ![]() |
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2 | 2 | ||||||
MIRT309180 | SPATA5 | spermatogenesis associated 5 | ![]() |
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2 | 2 | ||||||
MIRT354483 | LRRC58 | leucine rich repeat containing 58 | ![]() |
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2 | 2 | ||||||
MIRT354710 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 2 | ||||||
MIRT361004 | CDC5L | cell division cycle 5 like | ![]() |
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2 | 4 | ||||||
MIRT366247 | VMA21 | VMA21, vacuolar ATPase assembly factor | ![]() |
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2 | 2 | ||||||
MIRT405774 | EIF5 | eukaryotic translation initiation factor 5 | ![]() |
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2 | 2 | ||||||
MIRT442640 | TBC1D12 | TBC1 domain family member 12 | ![]() |
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2 | 2 | ||||||
MIRT443928 | ZNF99 | zinc finger protein 99 | ![]() |
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2 | 2 | ||||||
MIRT454287 | FXN | frataxin | ![]() |
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2 | 2 | ||||||
MIRT454367 | ASAH2 | N-acylsphingosine amidohydrolase 2 | ![]() |
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2 | 2 | ||||||
MIRT463574 | ZBTB39 | zinc finger and BTB domain containing 39 | ![]() |
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2 | 6 | ||||||
MIRT464484 | UGCG | UDP-glucose ceramide glucosyltransferase | ![]() |
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2 | 2 | ||||||
MIRT466866 | STX6 | syntaxin 6 | ![]() |
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2 | 2 | ||||||
MIRT467283 | SPNS1 | sphingolipid transporter 1 (putative) | ![]() |
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2 | 2 | ||||||
MIRT470298 | PPTC7 | PTC7 protein phosphatase homolog | ![]() |
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2 | 2 | ||||||
MIRT471630 | PAPD7 | poly(A) RNA polymerase D7, non-canonical | ![]() |
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2 | 2 | ||||||
MIRT472802 | MTMR4 | myotubularin related protein 4 | ![]() |
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2 | 4 | ||||||
MIRT474708 | KIF3A | kinesin family member 3A | ![]() |
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2 | 2 | ||||||
MIRT478256 | DDX3X | DEAD-box helicase 3, X-linked | ![]() |
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2 | 2 | ||||||
MIRT479330 | CERS2 | ceramide synthase 2 | ![]() |
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2 | 2 | ||||||
MIRT480658 | BSCL2 | BSCL2, seipin lipid droplet biogenesis associated | ![]() |
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2 | 2 | ||||||
MIRT481954 | ANKRD11 | ankyrin repeat domain 11 | ![]() |
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2 | 2 | ||||||
MIRT482895 | IAH1 | isoamyl acetate-hydrolyzing esterase 1 homolog | ![]() |
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2 | 4 | ||||||
MIRT493634 | HIC2 | HIC ZBTB transcriptional repressor 2 | ![]() |
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2 | 2 | ||||||
MIRT500847 | SYPL1 | synaptophysin like 1 | ![]() |
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2 | 4 | ||||||
MIRT502035 | LRIG2 | leucine rich repeats and immunoglobulin like domains 2 | ![]() |
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2 | 2 | ||||||
MIRT502185 | IGSF3 | immunoglobulin superfamily member 3 | ![]() |
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2 | 4 | ||||||
MIRT502605 | DNAJB9 | DnaJ heat shock protein family (Hsp40) member B9 | ![]() |
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2 | 10 | ||||||
MIRT502977 | CCNL1 | cyclin L1 | ![]() |
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2 | 8 | ||||||
MIRT504725 | PLEKHA6 | pleckstrin homology domain containing A6 | ![]() |
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2 | 10 | ||||||
MIRT504778 | CLEC2D | C-type lectin domain family 2 member D | ![]() |
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2 | 4 | ||||||
MIRT505786 | SATB1 | SATB homeobox 1 | ![]() |
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2 | 4 | ||||||
MIRT510090 | PPWD1 | peptidylprolyl isomerase domain and WD repeat containing 1 | ![]() |
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2 | 4 | ||||||
MIRT520010 | YY1 | YY1 transcription factor | ![]() |
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2 | 4 | ||||||
MIRT532552 | TXNL1 | thioredoxin like 1 | ![]() |
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2 | 2 | ||||||
MIRT533433 | TRPS1 | transcriptional repressor GATA binding 1 | ![]() |
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2 | 2 | ||||||
MIRT537459 | FAM84B | family with sequence similarity 84 member B | ![]() |
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2 | 2 | ||||||
MIRT541825 | SV2B | synaptic vesicle glycoprotein 2B | ![]() |
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2 | 2 | ||||||
MIRT543222 | TMEM117 | transmembrane protein 117 | ![]() |
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2 | 2 | ||||||
MIRT551088 | DDX52 | DExD-box helicase 52 | ![]() |
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2 | 2 | ||||||
MIRT551500 | UGT2B4 | UDP glucuronosyltransferase family 2 member B4 | ![]() |
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2 | 2 | ||||||
MIRT552326 | ZNF791 | zinc finger protein 791 | ![]() |
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2 | 2 | ||||||
MIRT553213 | TXLNG | taxilin gamma | ![]() |
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2 | 2 | ||||||
MIRT554590 | RRAGC | Ras related GTP binding C | ![]() |
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2 | 2 | ||||||
MIRT559004 | CA8 | carbonic anhydrase 8 | ![]() |
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2 | 2 | ||||||
MIRT559134 | BTG3 | BTG anti-proliferation factor 3 | ![]() |
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2 | 4 | ||||||
MIRT559409 | GDNF | glial cell derived neurotrophic factor | ![]() |
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2 | 4 | ||||||
MIRT560678 | SRFBP1 | serum response factor binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT560954 | POTED | POTE ankyrin domain family member D | ![]() |
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2 | 2 | ||||||
MIRT562856 | C17orf58 | chromosome 17 open reading frame 58 | ![]() |
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2 | 2 | ||||||
MIRT563003 | MOCS2 | molybdenum cofactor synthesis 2 | ![]() |
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2 | 2 | ||||||
MIRT564545 | CCDC80 | coiled-coil domain containing 80 | ![]() |
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2 | 2 | ||||||
MIRT566272 | PTAR1 | protein prenyltransferase alpha subunit repeat containing 1 | ![]() |
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2 | 2 | ||||||
MIRT566510 | PAWR | pro-apoptotic WT1 regulator | ![]() |
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2 | 2 | ||||||
MIRT572103 | EFNB2 | ephrin B2 | ![]() |
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2 | 2 | ||||||
MIRT574576 | NLGN4X | neuroligin 4, X-linked | ![]() |
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2 | 4 | ||||||
MIRT576574 | Serpine1 | serine (or cysteine) peptidase inhibitor, clade E, member 1 | ![]() |
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2 | 2 | ||||||
MIRT610815 | POT1 | protection of telomeres 1 | ![]() |
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2 | 2 | ||||||
MIRT624589 | BCL11B | B-cell CLL/lymphoma 11B | ![]() |
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2 | 2 | ||||||
MIRT627567 | SMAD6 | SMAD family member 6 | ![]() |
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2 | 2 | ||||||
MIRT632675 | MTX3 | metaxin 3 | ![]() |
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2 | 2 | ||||||
MIRT689265 | WDR83OS | WD repeat domain 83 opposite strand | ![]() |
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2 | 2 | ||||||
MIRT694310 | COPB2 | coatomer protein complex subunit beta 2 | ![]() |
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2 | 2 | ||||||
MIRT697721 | USP8 | ubiquitin specific peptidase 8 | ![]() |
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2 | 2 | ||||||
MIRT700209 | RFWD3 | ring finger and WD repeat domain 3 | ![]() |
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2 | 2 | ||||||
MIRT704399 | CTSS | cathepsin S | ![]() |
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2 | 2 | ||||||
MIRT710665 | CSTF2T | cleavage stimulation factor subunit 2 tau variant | ![]() |
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2 | 2 | ||||||
MIRT711953 | SLC7A14 | solute carrier family 7 member 14 | ![]() |
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2 | 2 | ||||||
MIRT712596 | ADCYAP1 | adenylate cyclase activating polypeptide 1 | ![]() |
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2 | 2 | ||||||
MIRT712692 | TNFAIP2 | TNF alpha induced protein 2 | ![]() |
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2 | 2 | ||||||
MIRT714171 | PPP1R2 | protein phosphatase 1 regulatory inhibitor subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT715964 | CES4A | carboxylesterase 4A | ![]() |
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2 | 2 | ||||||
MIRT722781 | PDE3A | phosphodiesterase 3A | ![]() |
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2 | 2 | ||||||
MIRT724505 | MSMO1 | methylsterol monooxygenase 1 | ![]() |
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2 | 2 |