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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctaggctgcaatcttcgtggttttttttttttttgcatgaacgaattcgattccgttgaattatttgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG

Basic information

species Zea mays
transcript GRMZM2G165351_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 11
----------------------gtaagtctaggctgcaatcttcgtg---gttttttttttttttgcatga--acgaattcgattccgttgaa---ttatttgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG
                        | |||||  ||   || |   |    |      | ||      ||||   | ||    |||   |  ||   ||| |   ||| |||||| ||||   |||| |||||  |||| |   ||||||||||||||||| |||||||||||||||| ||||
gttagtctcgcaaagaaaaagaaaaggtctattcttacatgtggatacaagcaagcatgttagagatatgactgctaacagtattttttcaaaatattaatctttttccagATATGATTGGGCTGCCAAGAAAAGCTTGCAAACTGGTTACTTTTTGTGGTCAATGGTGGCCTATGGTTCTG
















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|149112294|gb|EE295193.2|EE295193
EST:     TTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: TTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|67025992|gb|CO454741.1|CO454741
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|149073466|gb|EE161770.2|EE161770
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|149060142|gb|EE157102.2|EE157102
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|149086581|gb|EE176124.2|EE176124
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|22819684|gb|BU499774.1|BU499774
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|211215781|gb|FL437227.1|FL437227
EST:     TGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: TGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|60356079|gb|DN223052.1|DN223052
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|91054682|gb|EB165100.1|EB165100
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|32843028|gb|CD982709.1|CD982709
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|31406182|gb|CD484914.1|CD484914
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|74234147|gb|DT642061.1|DT642061
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|67024697|gb|CO453446.1|CO453446
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|32848049|gb|CD987730.1|CD987730
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
EST: gi|67017568|gb|CO446317.1|CO446317
EST:     GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAG                         ATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC
genomic: GGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGC

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), 48 (downstream exon)
Score: 181

TGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 130

TGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 180

TGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTGGTGATATCCTTCTTCCTGGTCTTTTAGTTGCTTTCTCGCTAAGgtaagtctag ... tgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttttttgcatgaacgaattcgattccgttgaattatttgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG
                                           tttgcttttc  CT-rich tract
                                      aattatttgctttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctaggctgcaatcttcgtggttttttttttttttgcatgaacgaattcgattccgttgaattatttgcttttcagATACGATTTTTCTGCAAAGAAGGGCTTACGGTCTGGTTACTTTTTGTGGGCAATGGTGGCCTATGGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG