Ased on RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsKamachi09_NSINE LINE LTR DNA Straightforward Low Complexity Satellite RNA Other Unknown AAGG TGTGATTGTGATSox2/uc008oxu.1 Regulatory Components Kamachi09_N2 sox2 Kamachi09_N5 Kamachi09_N1 Tomioka02_Sikorska08_SRR1_ Kamachi09_neural_Lef1_Lef1_ Takanaga09_Gli2?_dna_not_matching Tomioka02_Oct4/6Sox_ Kamachi09_neural_FGF_ Foshay08_Stat3_1_ Takanaga09_Gli_1_ Catena04_Oct4_Brn1/2_1_ Catena04_Oct4_Brn1/2_2_ MorenoM10_HRE_HIF1alpha_1_ MorenoM10_HRE_HIF1alpha_2_ Foshay08_Stat3_2_ Wiebe00_NF-Y_ Tomioka02 Sikorska08 SRR2 MicroRNAs from miRBase mmu-mir-1897 Repeating Components by RepeatMaskerKamachi09_NCGCACA AG CTCC AAAAAC TC CCTCCCTTCCTT CCTT CA 22xTC 18xCA 29xAGCT TGACTTTGSimple Tandem Repeats by TRF T AAAACAAA CCTAGCTCTGGCC…CACT AGCA GA AC GGGGAA AGAC TGGGGG AGACAGGC 16xCA 19xACCA18xACMicrosatellites – Di-nucleotide and Tri-nucleotide Repeats GC % in 5-Base Windows22xCA 16xCT70 _ GC PercentRepressor Element 1-Silencing Transcription 4-Hydroperoxy cyclophosphamide Reactive Oxygen Species Aspect (REST) binding web sites Regulatory elements from ORegAnnoFigure 3 The Sox2 Regulatory Area: Regulation and Repeats. The Sox2 regulatory area, displayed employing the UCSC genome browser. See Figure 1 for further information. On top, the Sox2 overlapping transcript called BC057611/uc008oxq.1 [81] is visualized, including one particular microRNA. SRR1 and SRR2 denote conserved regions identified by [82] and [83].Fuellen and Struckmann Biology Direct 2010, five:67 http://www.biology-direct.com/content/5/1/Page 6 ofScale chr3: BC057611/uc008oxq.34535000 AK045614/uc008oxr.1 AK039272/uc008oxs.1 AK031919/uc008oxt.20 kb 34545000 34550000 34555000 34560000 34565000 UCSC Genes According to RefSeq, UniProt, GenBank, CCDS and Comparative GenomicsKamachi09_NSox2/uc008oxu.1 Regulatory Components Kamachi09_N2 sox2 Kamachi09_N5 Kamachi09_N1 Tomioka02_Sikorska08_SRR1_ Kamachi09_neural_Lef1_Lef1_ Takanaga09_Gli2?_dna_not_matching Tomioka02_Oct4/6Sox_ Kamachi09_neural_FGF_ Foshay08_Stat3_1_ Takanaga09_Gli_1_ Catena04_Oct4_Brn1/2_1_ Catena04_Oct4_Brn1/2_2_ MorenoM10_HRE_HIF1alpha_1_ MorenoM10_HRE_HIF1alpha_2_ Foshay08_Stat3_2_ Wiebe00_NF-Y_ Tomioka02 Sikorska08 SRR2 30-Way Multiz Alignment ConservationKamachi09_NMammal Cons Euarch Cons Vertebrate Cons Rat Guinea_pig Rabbit Human Chimp Rhesus Orangutan Marmoset Bushbaby Tree_shrew Shrew Aggrecan Inhibitors targets Hedgehog Dog Cat Horse Cow Armadillo Elephant Tenrec Opossum Platypus Chicken Lizard X_tropicalis Stickleback Zebrafish Tetraodon Fugu MedakaFigure four The Sox2 Regulatory Region: Conservation. The Sox2 regulatory region, displayed using the UCSC genome browser. See Figure two for further information and facts.identical gene at Ensembl, exactly where mouse-over from the gene enables a popup window in which a visualization of your gene could be started. From there, we obtained the Ensembl Compara gene tree using the link known as “Gene Tree (image)”, on the left.Gene Expression DataWe inspected all four UCSC sets of tracks visualizing gene expression information that happen to be obtainable within the UCSC mm9 tracks (GNF Expression Atlas two [43], GNF Expression Atlas on Mouse Affymetrix U74A Chip, GNF Expression Atlas onScale chr6:2 kb 122654000 122654500 122655000 122655500 122656000 122656500 122657000 UCSC Genes Depending on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics Regulatory Elements Gu05_Gcnf_ Lin05_p53_RE1_122657500 Nanog LOCChen09_R(Cdx2_and_Nanog)CR3_ CR2_ Jiang08_Klf_ Suzuki06_Stat_ Suzuki06_T_Pereira06_Tcf3_SINE LINE LTR DNA Uncomplicated Low Complexity Satellite RNA Other Unknown GA 37xGAMicroRNAs from.
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