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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcgtcttgtttattagtctaattatctagatgatacatttcttctgtagagtatgtccatggaatcagatttaattttaaacacattattgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA

Basic information

species Zea mays
transcript GRMZM2G052875_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 10
------cttcgtcttg--tttattagtctaattatctagatgatacatttcttctgtagagtatgtccatggaatcagatttaattttaaacacattattgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA
      ||   | |||  || || ||  | ||  ||||| | ||| |||  ||        || | | ||   ||   | ||||||  |   | |  ||| |||||||| || || ||||||||||||| ||||||||||||||||||||||| |||||| || ||
ggtattctagatgttgacttcatcagagttat-gtctagttcatatattattt------gataggcctataatattgaaattaattgaaggaatac-attcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA
















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|211535329|gb|FL357693.1|FL357693
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|211178585|gb|FL326372.1|FL326372
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTGAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGNGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|211376351|gb|FL146644.1|FL146644
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|211084967|gb|FL399106.1|FL399106
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|211376352|gb|FL146645.1|FL146645
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|211072830|gb|FL342711.1|FL342711
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|31359162|gb|CD443519.1|CD443519
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTG                         GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG
genomic: AATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaat ... ttgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtagagtatgtccatggaatcagatttaattttaaacacattattgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA
                         atttaat  putative branch site (score: 4)
                   aatcagatttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcgtcttgtttattagtctaattatctagatgatacatttcttctgtagagtatgtccatggaatcagatttaattttaaacacattattgttattagGCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaca