pre-miRNA Information | |
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pre-miRNA | hsa-mir-4436b-1 |
Genomic Coordinates | chr2: 110086433 - 110086523 |
Description | Homo sapiens miR-4436b-1 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | hsa-mir-4436b-2 |
Genomic Coordinates | chr2: 110284853 - 110284943 |
Description | Homo sapiens miR-4436b-2 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||
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Mature miRNA | hsa-miR-4436b-3p | ||||||
Sequence | 60| CAGGGCAGGAAGAAGUGGACAA |81 | ||||||
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 | THBD | ||||||||||||||||||||
Synonyms | AHUS6, BDCA3, CD141, THPH12, THRM, TM | ||||||||||||||||||||
Description | thrombomodulin | ||||||||||||||||||||
Transcript | NM_000361 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on THBD | |||||||||||||||||||||
3'UTR of THBD (miRNA target sites are highlighted) |
>THBD|NM_000361|3'UTR 1 GCGGCCTCCGTCCAGGAGCCTGGCTCCGTCCAGGAGCCTGTGCCTCCTCACCCCCAGCTTTGCTACCAAAGCACCTTAGC 81 TGGCATTACAGCTGGAGAAGACCCTCCCCGCACCCCCCAAGCTGTTTTCTTCTATTCCATGGCTAACTGGCGAGGGGGTG 161 ATTAGAGGGAGGAGAATGAGCCTCGGCCTCTTCCGTGACGTCACTGGACCACTGGGCAATGATGGCAATTTTGTAACGAA 241 GACACAGACTGCGATTTGTCCCAGGTCCTCACTACCGGGCGCAGGAGGGTGAGCGTTATTGGTCGGCAGCCTTCTGGGCA 321 GACCTTGACCTCGTGGGCTAGGGATGACTAAAATATTTATTTTTTTTAAGTATTTAGGTTTTTGTTTGTTTCCTTTGTTC 401 TTACCTGTATGTCTCCAGTATCCACTTTGCACAGCTCTCCGGTCTCTCTCTCTCTACAAACTCCCACTTGTCATGTGACA 481 GGTAAACTATCTTGGTGAATTTTTTTTTCCTAGCCCTCTCACATTTATGAAGCAAGCCCCACTTATTCCCCATTCTTCCT 561 AGTTTTCTCCTCCCAGGAACTGGGCCAACTCACCTGAGTCACCCTACCTGTGCCTGACCCTACTTCTTTTGCTCTTAGCT 641 GTCTGCTCAGACAGAACCCCTACATGAAACAGAAACAAAAACACTAAAAATAAAAATGGCCATTTGCTTTTTCACCAGAT 721 TTGCTAATTTATCCTGAAATTTCAGATTCCCAGAGCAAAATAATTTTAAACAAAGGTTGAGATGTAAAAGGTATTAAATT 801 GATGTTGCTGGACTGTCATAGAAATTACACCCAAAGAGGTATTTATCTTTACTTTTAAACAGTGAGCCTGAATTTTGTTG 881 CTGTTTTGATTTGTACTGAAAAATGGTAATTGTTGCTAATCTTCTTATGCAATTTCCTTTTTTGTTATTATTACTTATTT 961 TTGACAGTGTTGAAAATGTTCAGAAGGTTGCTCTAGATTGAGAGAAGAGACAAACACCTCCCAGGAGACAGTTCAAGAAA 1041 GCTTCAAACTGCATGATTCATGCCAATTAGCAATTGACTGTCACTGTTCCTTGTCACTGGTAGACCAAAATAAAACCAGC 1121 TCTACTGGTCTTGTGGAATTGGGAGCTTGGGAATGGATCCTGGAGGATGCCCAATTAGGGCCTAGCCTTAATCAGGTCCT 1201 CAGAGAATTTCTACCATTTCAGAGAGGCCTTTTGGAATGTGGCCCCTGAACAAGAATTGGAAGCTGCCCTGCCCATGGGA 1281 GCTGGTTAGAAATGCAGAATCCTAGGCTCCACCCCATCCAGTTCATGAGAATCTATATTTAACAAGATCTGCAGGGGGTG 1361 TGTCTGCTCAGTAATTTGAGGACAACCATTCCAGACTGCTTCCAATTTTCTGGAATACATGAAATATAGATCAGTTATAA 1441 GTAGCAGGCCAAGTCAGGCCCTTATTTTCAAGAAACTGAGGAATTTTCTTTGTGTAGCTTTGCTCTTTGGTAGAAAAGGC 1521 TAGGTACACAGCTCTAGACACTGCCACACAGGGTCTGCAAGGTCTTTGGTTCAGCTAAGCTAGGAATGAAATCCTGCTTC 1601 AGTGTATGGAAATAAATGTATCATAGAAATGTAACTTTTGTAAGACAAAGGTTTTCCTCTTCTATTTTGTAAACTCAAAA 1681 TATTTGTACATAGTTATTTATTTATTGGAGATAATCTAGAACACAGGCAAAATCCTTGCTTATGACATCACTTGTACAAA 1761 ATAAACAAATAACAATGTGCTCTCGGGTTGTGTGTCTGTTCACTTTTCCTCCCTCAGTGCCCTCATTTTATGTCATTAAA 1841 TGGGGCTCACAAACCATGCAAATGCTATGAGATGCATGGAGGGCTGCCCTGTACCCCAGCACTTGTGTTGTCTGGTGGTG 1921 GCACCATCTCTGATTTTCAAAGCTTTTTCCAGAGGCTATTATTTTCACTGTAGAATGATTTCATGCTATCTCTGTGTGCA 2001 CAAATATTTATTTTCTTTCTGTAACCATAACAACTTCATATATGAGGACTTGTGTCTCTGTGCTTTTAAATGCATAAATG 2081 CATTATAGGATCATTTGTTGGAATGAATTAAATAAACCCTTCCTGGGGCATCTGGCGAATCCCAAAAAAAAAAAAAAAAA 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 | 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 GSM1084066. RNA binding protein: AGO2. Condition:CLIP_noemetine_SantaCruzAb
HITS-CLIP data was present in GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb
HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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]
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CLIP-seq Support 1 for dataset GSM4903832 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Human neurons / 124TD_shELAVL3_b |
Location of target site | NM_000361 | 3UTR | UGGAAGCUGCCCUGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161238 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1084066 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SantaCruzAb |
Location of target site | ENST00000377103.2 | 3UTR | ACAAGAAUUGGAAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM1084067 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SantaCruzAb |
Location of target site | ENST00000377103.2 | 3UTR | ACAAGAAUUGGAAGCUGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1084069 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SigmaAb |
Location of target site | ENST00000377103.2 | 3UTR | ACAAGAAUUGGAAGCU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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87 hsa-miR-4436b-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT066957 | ATXN7L3B | ataxin 7 like 3B | ![]() |
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2 | 8 | ||||||
MIRT119284 | NABP1 | nucleic acid binding protein 1 | ![]() |
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2 | 6 | ||||||
MIRT128915 | KMT2A | lysine methyltransferase 2A | ![]() |
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2 | 2 | ||||||
MIRT150116 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT173040 | YTHDF3 | YTH N6-methyladenosine RNA binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT253117 | BCL2L12 | BCL2 like 12 | ![]() |
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2 | 2 | ||||||
MIRT256997 | RGMB | repulsive guidance molecule family member b | ![]() |
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2 | 2 | ||||||
MIRT259746 | SNX12 | sorting nexin 12 | ![]() |
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2 | 2 | ||||||
MIRT267278 | TMEM109 | transmembrane protein 109 | ![]() |
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2 | 2 | ||||||
MIRT441934 | C1orf109 | chromosome 1 open reading frame 109 | ![]() |
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2 | 2 | ||||||
MIRT443625 | CPSF2 | cleavage and polyadenylation specific factor 2 | ![]() |
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2 | 2 | ||||||
MIRT445757 | AGO1 | argonaute 1, RISC catalytic component | ![]() |
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2 | 2 | ||||||
MIRT447835 | CTIF | cap binding complex dependent translation initiation factor | ![]() |
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2 | 2 | ||||||
MIRT451230 | ZNF444 | zinc finger protein 444 | ![]() |
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2 | 2 | ||||||
MIRT451966 | TMPRSS5 | transmembrane protease, serine 5 | ![]() |
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2 | 2 | ||||||
MIRT453127 | HOXC4 | homeobox C4 | ![]() |
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2 | 2 | ||||||
MIRT454604 | RPL13A | ribosomal protein L13a | ![]() |
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2 | 2 | ||||||
MIRT455176 | SUV39H1 | suppressor of variegation 3-9 homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT455547 | GJB1 | gap junction protein beta 1 | ![]() |
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2 | 2 | ||||||
MIRT458197 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT458356 | NOC2L | NOC2 like nucleolar associated transcriptional repressor | ![]() |
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2 | 2 | ||||||
MIRT458923 | DNM2 | dynamin 2 | ![]() |
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2 | 2 | ||||||
MIRT461013 | SYT7 | synaptotagmin 7 | ![]() |
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2 | 2 | ||||||
MIRT461643 | ZSWIM4 | zinc finger SWIM-type containing 4 | ![]() |
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2 | 2 | ||||||
MIRT461997 | PACSIN1 | protein kinase C and casein kinase substrate in neurons 1 | ![]() |
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2 | 2 | ||||||
MIRT462367 | BCL7B | BCL tumor suppressor 7B | ![]() |
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2 | 2 | ||||||
MIRT464915 | TXNIP | thioredoxin interacting protein | ![]() |
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2 | 2 | ||||||
MIRT466311 | TIMM22 | translocase of inner mitochondrial membrane 22 | ![]() |
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2 | 2 | ||||||
MIRT466591 | TBC1D2B | TBC1 domain family member 2B | ![]() |
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2 | 2 | ||||||
MIRT467045 | SRSF1 | serine and arginine rich splicing factor 1 | ![]() |
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2 | 2 | ||||||
MIRT468750 | SDC2 | syndecan 2 | ![]() |
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2 | 2 | ||||||
MIRT468943 | RPS24 | ribosomal protein S24 | ![]() |
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2 | 2 | ||||||
MIRT469474 | REEP5 | receptor accessory protein 5 | ![]() |
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2 | 2 | ||||||
MIRT469913 | PTRF | caveolae associated protein 1 | ![]() |
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2 | 2 | ||||||
MIRT473325 | MEX3A | mex-3 RNA binding family member A | ![]() |
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2 | 2 | ||||||
MIRT473643 | MARK2 | microtubule affinity regulating kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT474064 | LMNB2 | lamin B2 | ![]() |
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2 | 2 | ||||||
MIRT474357 | KMT2D | lysine methyltransferase 2D | ![]() |
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2 | 2 | ||||||
MIRT475394 | ICMT | isoprenylcysteine carboxyl methyltransferase | ![]() |
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2 | 4 | ||||||
MIRT476335 | GLTSCR1L | BRD4 interacting chromatin remodeling complex associated protein like | ![]() |
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2 | 2 | ||||||
MIRT478651 | CTDNEP1 | CTD nuclear envelope phosphatase 1 | ![]() |
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2 | 2 | ||||||
MIRT479585 | CDC42SE1 | CDC42 small effector 1 | ![]() |
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2 | 2 | ||||||
MIRT479943 | CBX5 | chromobox 5 | ![]() |
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2 | 2 | ||||||
MIRT482001 | AMOTL2 | angiomotin like 2 | ![]() |
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2 | 2 | ||||||
MIRT482043 | AMER1 | APC membrane recruitment protein 1 | ![]() |
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2 | 2 | ||||||
MIRT483070 | EXT2 | exostosin glycosyltransferase 2 | ![]() |
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2 | 6 | ||||||
MIRT484323 | KCNH1 | potassium voltage-gated channel subfamily H member 1 | ![]() |
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2 | 4 | ||||||
MIRT487528 | GXYLT2 | glucoside xylosyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT489636 | ALS2CL | ALS2 C-terminal like | ![]() |
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2 | 2 | ||||||
MIRT490693 | SSTR1 | somatostatin receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT490871 | UPK2 | uroplakin 2 | ![]() |
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2 | 2 | ||||||
MIRT492582 | PPM1L | protein phosphatase, Mg2+/Mn2+ dependent 1L | ![]() |
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2 | 2 | ||||||
MIRT492945 | NEUROD2 | neuronal differentiation 2 | ![]() |
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2 | 2 | ||||||
MIRT498675 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 4 | ||||||
MIRT499349 | RAB25 | RAB25, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT502338 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 4 | ||||||
MIRT502976 | CCNL1 | cyclin L1 | ![]() |
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2 | 8 | ||||||
MIRT503706 | NUP62 | nucleoporin 62 | ![]() |
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2 | 2 | ||||||
MIRT505567 | SMUG1 | single-strand-selective monofunctional uracil-DNA glycosylase 1 | ![]() |
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2 | 2 | ||||||
MIRT507808 | CDKN1B | cyclin dependent kinase inhibitor 1B | ![]() |
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2 | 2 | ||||||
MIRT513242 | FBXO41 | F-box protein 41 | ![]() |
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2 | 6 | ||||||
MIRT513586 | EVX1 | even-skipped homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT525036 | FRK | fyn related Src family tyrosine kinase | ![]() |
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2 | 2 | ||||||
MIRT531035 | TDGF1P3 | teratocarcinoma-derived growth factor 1 pseudogene 3 | ![]() |
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2 | 2 | ||||||
MIRT531939 | RBMS2 | RNA binding motif single stranded interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT534912 | PUM2 | pumilio RNA binding family member 2 | ![]() |
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2 | 2 | ||||||
MIRT535717 | N4BP1 | NEDD4 binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT540498 | ZMAT4 | zinc finger matrin-type 4 | ![]() |
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2 | 4 | ||||||
MIRT541465 | AURKA | aurora kinase A | ![]() |
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2 | 2 | ||||||
MIRT554328 | SH3GLB1 | SH3 domain containing GRB2 like, endophilin B1 | ![]() |
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2 | 2 | ||||||
MIRT561572 | SLC6A9 | solute carrier family 6 member 9 | ![]() |
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2 | 2 | ||||||
MIRT564715 | ZNF322P1 | zinc finger protein 322 pseudogene 1 | ![]() |
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2 | 2 | ||||||
MIRT576176 | Hmox1 | heme oxygenase 1 | ![]() |
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2 | 2 | ||||||
MIRT629712 | XKR4 | XK related 4 | ![]() |
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2 | 2 | ||||||
MIRT636182 | THBD | thrombomodulin | ![]() |
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2 | 2 | ||||||
MIRT646315 | MPHOSPH8 | M-phase phosphoprotein 8 | ![]() |
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2 | 2 | ||||||
MIRT649174 | IQSEC1 | IQ motif and Sec7 domain 1 | ![]() |
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2 | 2 | ||||||
MIRT666945 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | ![]() |
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2 | 2 | ||||||
MIRT684057 | FOLR1 | folate receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT687585 | MAU2 | MAU2 sister chromatid cohesion factor | ![]() |
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2 | 2 | ||||||
MIRT689953 | ZNF185 | zinc finger protein 185 with LIM domain | ![]() |
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2 | 2 | ||||||
MIRT704071 | SRCAP | Snf2 related CREBBP activator protein | ![]() |
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2 | 2 | ||||||
MIRT704327 | DCUN1D5 | defective in cullin neddylation 1 domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT705406 | ATP1B3 | ATPase Na+/K+ transporting subunit beta 3 | ![]() |
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2 | 2 | ||||||
MIRT710488 | CDH5 | cadherin 5 | ![]() |
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2 | 2 | ||||||
MIRT718241 | LCE1A | late cornified envelope 1A | ![]() |
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2 | 2 | ||||||
MIRT723182 | CDCA4 | cell division cycle associated 4 | ![]() |
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2 | 2 |