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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagcttcagctaaacttcactgttgaacttttcattcaactcatatttcttataagtagatgagctattattgacttgtttcttacaatatgacag

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 5'ss of exon 13
TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagcttcagctaaacttcactgttgaacttttcattcaactcatatttcttataagtagatgagctattattgacttgtttcttac-aatatgacag--
|||||| ||||||||||| || ||| |||| |||||||||||||| |||||||| || ||| |||||||||||||||||||||||||||| |||||  ||||||||||  |||       |||  || ||||||    | ||      ||||||  ||   |||||| ||  ||     ||   | |   |  |   ||||    
TGTTGAGATAAGAGAGGAAGTGGGACAAGAAAATTTCTTCCTTTTTGGTGCCAAGGCAGATCAAGTTGCTGGGCTGAGGAAGGATAGAGAGAATGGCTTGgtaagatattttctttctttcttt-cttttgaacgaagc-ttggtaagatattttcta---gtagataagtgatatacaaccattattagatgagcttgacttgc

upper sequence: GRMZM2G085577_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 5'ss of exon 14
TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagcttcagctaaacttcactgttgaacttttcattc------aactcatatttcttataa----gtagatgagctattattgact------tgtttctta---caatatgacag--------------------------------
|||||| ||||||||||||||||| ||||| |||||||| ||||| ||||| |  |||||| | ||  || | ||| | || ||  ||||| | || |||||| |  |   ||  ||   || |  |    || ||||  |        |||  ||       |  |     |  | |  ||  || ||| |      || ||||       || |||||                                 
TGTTGAGATAAGAGAGGAGGTTGGCGAAGAAAATTTCTTTCTTTTTGGTGCAACGGCCGATCAGGTCCCTCGACTGCGTAAAGAACGAGAAGACGGACTGgtatgtcactctctccttttctcccttacataaatttttgtctctgtggaacaaatgcgagccaccataccatgaaaggccttataatgaatcacctatgcttctggactttatctgacatgaaacgtttttgtgcctgtaaaaactgattag
















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|91049536|gb|EB159954.1|EB159954
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|93283527|gb|EB675791.1|EB675791
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|211014837|gb|FL417332.1|FL417332
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|211209895|gb|FL408331.1|FL408331
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|67041226|gb|CO467481.1|CO467481
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCATTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|71301961|gb|DR787056.1|DR787056
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60358978|gb|DN225951.1|DN225951
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAATCATTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|76924589|gb|DV170028.1|DV170028
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|32855932|gb|CD995613.1|CD995613
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGACAGAGAAAATGGCCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|211355999|gb|FL410711.1|FL410711
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60354851|gb|DN221824.1|DN221824
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60354619|gb|DN221592.1|DN221592
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|40335159|gb|CK369229.1|CK369229
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGACAGAGAAAATGGCCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60347330|gb|DN214303.1|DN214303
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|71301958|gb|DR787055.1|DR787055
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60401276|gb|DN234083.1|DN234083
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|6636976|gb|AW261248.1|AW261248
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|94472102|gb|EB701060.1|EB701060
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|211204436|gb|FL394622.1|FL394622
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|37380429|gb|CF627026.1|CF627026
EST:     TGGGCTGAGGAAGGACAGAGAAAATGGCCTG                         TTCAAACCAGACCCACG-TTTGAAAGAAGCCAAGCAGTTTATAAGGAGTGG
genomic: TGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTG-AAGAAGCCAAGCAGTTTATAAGGAGTGG
EST: gi|60348694|gb|DN215667.1|DN215667
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|19770331|gb|BQ035052.1|BQ035052
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACG-TTTGAAGAAGCCAAGCAG-TTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|71767179|gb|DR965116.1|DR965116
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|211521628|gb|FL412959.1|FL412959
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|60340741|gb|DN207714.1|DN207714
EST:     C-AAGCCGATGAAGTTGCTGNGGCTGAGGAAGGATAGAGAAAATGGTCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
genomic: CAAAGCCGATGAAGTTGCTG-GGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|89106551|gb|DY576768.1|DY576768
EST:     CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGACAGAGAAAATGGCCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAACAGTTTATAAGGAGTGGC
genomic: CCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC
EST: gi|19436465|gb|BM952875.1|BM952875
EST:     AGAGAAAATGGCCTG                         TTCAAACCAGACCCACGTTTTGAAGAAGCCAAACAGTTTATAAGGAGTGGC
genomic: AGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 362

TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGCGCTTTTGGCAGCTATGACTATGAACCTCTCTTGGATTCCCTTGAAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGCGCTTTTGGCAGCTATGACTATGAACCTCTCTTGGATTCCCTTGAAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGCGCTTTTGGCAGCTATGACTATGAACCTCTCTTGGATTCCCTTGAAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

TGTTGAAATAAGAGAGGAGGTTGGAGAAGATAATTTCTTCCTTTTCGGTGCCAAAGCCGATGAAGTTGCTGGGCTGAGGAAGGATAGAGAAAATGGTCTGgtaagatagc ... aatatgacagTTCAAACCAGACCCACGTTTTGAAGAAGCCAAGCAGTTTATAAGGAGTGGCGCTTTTGGCAGCTATGACTATGAACCTCTCTTGGATTCCCTTGAAGGGA