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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggatgtgaatggttcattcttttgtagttcataacctaaaatatgaatcgagttgagagcaaggtattttacttatacgattctcactaacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG

Basic information

species Zea mays
transcript GRMZM2G330650_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g25390.1 (Oryza sativa), 3'ss of exon 5
gaggatgtgaatggttcattcttttgtagttcataacctaaaatatgaatcgagttgagagcaaggtattt-tacttatacgatt--ctcactaacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG
  || | |   ||| |||||  | | ||   |     | |  | |  |    |    |||      | ||  | |||||   ||   ||  ||||  ||||||| |||||||| |||||||| || ||| | |||||  | ||||||   || || |||||||||||||| ||||||||||||
--gggttttgctggctcattgatct-tatcacgctgacaatgacactatggaaagctagatatctctgttagttcttatgtaatcacctgtctaaacttgcagCTATGACAAACCAACAACTGATGGATGCTGGAAGAGAACAAATGACTCAGACTGATCAAGCTATTGACCGTTCAAAAATG

upper sequence: GRMZM2G330650_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g25390.3 (Oryza sativa), 3'ss of exon 5
gaggatgtgaatggttcattcttttgtagttcataacctaaaatatgaatcgagttgagagcaaggtattt-tacttatacgatt--ctcactaacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG--------------------
  || | |   ||| |||||  | | ||   |     | |  | |  |    |    |||      | ||  | |||||   ||   ||  ||||  ||||||| |||||||| |||||||| || ||| | |||||  | ||||||   || || |||||||||||||| ||||||||||||                    
--gggttttgctggctcattgatct-tatcacgctgacaatgacactatggaaagctagatatctctgttagttcttatgtaatcacctgtctaaacttgcagCTATGACAAACCAACAACTGATGGATGCTGGAAGAGAACAAATGACTCAGACTGATCAAGCTATTGACCGTTCAAAAATGGTTGCTTTACGAACTACACT
















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|71774532|gb|DR972410.1|DR972410
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|60396385|gb|DN229254.1|DN229254
EST:     GAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: GAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|32866170|gb|CF005852.1|CF005852
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATGCGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|50338100|gb|CO533226.1|CO533226
EST:     GCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: GCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|60396054|gb|DN228924.1|DN228924
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|78122353|gb|DV540737.1|DV540737
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|211141939|gb|FL417378.1|FL417378
EST:     ATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: ATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|211019324|gb|FL371811.1|FL371811
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|7135269|gb|AW498001.1|AW498001
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|211320442|gb|FL345947.1|FL345947
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAA
EST: gi|78122352|gb|DV540736.1|DV540736
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|32827094|gb|CD966772.1|CD966772
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATGCGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|60337886|gb|DN204859.1|DN204859
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|148961350|gb|EE012080.2|EE012080
EST:     TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: TGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
EST: gi|76019098|gb|DT946268.1|DT946268
EST:     AGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAG                         CCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA
genomic: AGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCATCAGgtgaaattag ... aacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatcgagttgagagcaaggtattttacttatacgattctcactaacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG
                                         cactaac  putative branch site (score: 1)
                     tattttacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggatgtgaatggttcattcttttgtagttcataacctaaaatatgaatcgagttgagagcaaggtattttacttatacgattctcactaacattgcagCCATGACAAATCAACAACTCATTGATACGGGAAGGAACCAAATGGACCAAACAGATCAAGCTATTGAACGTTCAAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT