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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgagcaagcgattgactgcatcaaatttatttccatggttcctgcacagttattcatcggaataacagtaaatttcaatcctttttcgtggatacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCC

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 17
gtaagtcgagcaagcgattgactg-catcaaatttatttccatggttcctgcacagttattcatcggaataacagtaaatttcaatcctttttcgtggatacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCC
         | | ||   | || | |||  || |||||      |||     ||   |||||||  || |||    || |   ||  | || |  | | | | ||  |||||||||| || |||||||| || ||| |  |||| ||| |   ||| |||||||| ||||||||||| || |||||||| |||||||||||||||||||
---------gtatgccgataaccgtcatggaaattattatttaagtta----acttctattcat--gattaatgacaattcataagacattattcttg-tgccatgcagTTGAGAGGATTTGAGATGCTAAAGGCAATTCACCTAGAGACAACGCCATTCAGCATAGAGAAGGACCTGGTGACTCCAACTTTTAAGCTCAAGAGACCCC
















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|9254901|gb|BE345369.1|BE345369
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|5670866|gb|AI932129.1|AI932129
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|76283291|gb|DV022859.1|DV022859
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|211099227|gb|FL470676.1|FL470676
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|4647598|gb|AI622673.1|AI622673
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32909558|gb|CF014370.1|CF014370
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|148958442|gb|EC904676.2|EC904676
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|60337173|gb|DN204146.1|DN204146
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|4647597|gb|AI622672.1|AI622672
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|86473157|gb|DY239527.1|DY239527
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32836844|gb|CD976522.1|CD976522
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|9254900|gb|BE345368.1|BE345368
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|20315387|gb|BQ169253.1|BQ169253
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|83279443|gb|DV943451.1|DV943451
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32837781|gb|CD977459.1|CD977459
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32909559|gb|CF014371.1|CF014371
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|71430908|gb|DR811958.1|DR811958
EST:     GGAAGAAACTTGGG                         TTGAGAGGTTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: GGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|13150470|gb|BG320792.1|BG320792
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAS-AGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|148999539|gb|EE036510.2|EE036510
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|74243995|gb|DT651909.1|DT651909
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|149086278|gb|EE175819.2|EE175819
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|211174079|gb|FL129194.1|FL129194
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32837912|gb|CD977590.1|CD977590
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|12972551|gb|BG268038.1|BG268038
EST:     GGACCTANCCGGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: GGACCTA--C-GTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|7145452|gb|AW506933.1|AW506933
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|149098381|gb|EE184357.2|EE184357
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|32867314|gb|CF006996.1|CF006996
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|213187833|gb|FM185065.1|FM185065
EST:     CGAGGAGCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|78544549|gb|DV622047.1|DV622047
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|149076510|gb|EE165136.2|EE165136
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|149085815|gb|EE175337.2|EE175337
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
EST: gi|94479493|gb|EB708451.1|EB708451
EST:     CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGG                         TTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC
genomic: CGAGGACCTACGTTCGGGATCAGCTGAACCAAACTGGGAAGAAACTTGGGgtaagtcgag ... tacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattcatcggaataacagtaaatttcaatcctttttcgtggatacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCC
            gaataac  putative branch site (score: 2)
             aataacagtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgagcaagcgattgactgcatcaaatttatttccatggttcctgcacagttattcatcggaataacagtaaatttcaatcctttttcgtggatacaatatagTTGAGAGGCTTCGAGATGCTGAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA