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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctgcctgcatttactacctattttgccttgtagtgttttccaaatgggccttatgtttcccaatttacttctgttaattacttctttgggggcacactcttctttcctgtttcactgctagaccttgatcttgtcttataatctggtcttttctaacattgattttttcag

Basic information

species Zea mays
transcript GRMZM2G107639_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 5'ss of exon 5
CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctgcctgcatttactacctattttgccttgtagtgttttccaaatgggccttatgtttcccaatttacttctgttaattacttctt-tgggggcacactcttctttcctgtttcactgctagaccttgatcttgtcttataatctggtcttttctaacattgattttttcag
||  |||||||||||||||| ||||| || ||| | ||||| ||  ||||||||||||||||||        ||||  | ||  | | ||| ||   |  | | || ||  |  | | | | | | ||  ||| | |||||  |||    ||| |   |  | ||| |                                                                       
CTGCGCAGAGAGAATAAGCTAACCAAGTCGTCAATTATGGTTACCTCTGGTGCAAATCAGgtaa--------tgcacatgctttccagttt-ccacctgatttattacagctttgtcatct-tattccggttttcctctgtgtattttgccttgtttagctagactatag---------------------------------------------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148932368|gb|EC876010.2|EC876010
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211260539|gb|FL346343.1|FL346343
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|78110709|gb|DV529107.1|DV529107
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGAGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|67030337|gb|CO459086.1|CO459086
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTATC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211010784|gb|FL361163.1|FL361163
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|148947797|gb|EC893285.2|EC893285
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211307790|gb|FL085771.1|FL085771
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCT
EST: gi|211111425|gb|FL330322.1|FL330322
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTKCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGT
EST: gi|211305768|gb|FL085761.1|FL085761
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACT
EST: gi|211307789|gb|FL085770.1|FL085770
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|148963140|gb|EE014107.2|EE014107
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|149112179|gb|EE295100.2|EE295100
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211307791|gb|FL085772.1|FL085772
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTG
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTG
EST: gi|149037081|gb|EE155270.2|EE155270
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211305763|gb|FL085756.1|FL085756
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCCTTTGTGAACTTGGTCCTCACTCTTTGTGATGC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGC
EST: gi|149084340|gb|EE173781.2|EE173781
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|76286951|gb|DV026519.1|DV026519
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|50325408|gb|CO520534.1|CO520534
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|148990980|gb|EE032414.2|EE032414
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211307793|gb|FL085774.1|FL085774
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTT-GTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATT
EST: gi|149014921|gb|EE044649.2|EE044649
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211448663|gb|FL323020.1|FL323020
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATG
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATG
EST: gi|211305634|gb|FL309433.1|FL309433
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATT
EST: gi|211305773|gb|FL085766.1|FL085766
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTG
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTG
EST: gi|211526539|gb|FL366365.1|FL366365
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|67011573|gb|CO440322.1|CO440322
EST:     TGGTCACTGCTGGTGCAAATCAC                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTATC
genomic: TGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211325052|gb|FL357886.1|FL357886
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
EST: gi|211305775|gb|FL085768.1|FL085768
EST:     AGAACAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTC
EST: gi|211305771|gb|FL085764.1|FL085764
EST:     AGAACAAGCTTACCAAATCATCTGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCT
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCT
EST: gi|148931036|gb|EC873618.2|EC873618
EST:     AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAG                         GCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC
genomic: AGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 44

CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 341

CTAAGCAGAGAGAATAAGCTTACCAAATCATCAGTCATGGTCACTGCTGGTGCAAATCAGgtaagttctg ... attttttcagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG