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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaatttttccatcttgatgattattccttgtaagattcattgtttttatgtgtataatctcacagttgttcatctacag

Basic information

species Zea mays
transcript GRMZM2G013750_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 3
TGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaatttttccatcttgatgatta-ttccttgtaagattcattgt--ttttatgtgtataatctcacagttgttcatctacag---
||| |||||||||||||||||||| |||||||| || || |||||||| ||||||||  | ||||||||||| ||  ||||||| || |||||||| |||||||||||  |  |  ||  |  |||  || | | ||||||| | ||   ||| |||||| ||||||||| | | | |||| || |   
TGCCATGGTTCAGAAAGCAATGGAGTACATTGACTTAACGCCAGACATGGACACACGTATTGAGCTAATCAAGACGTTGAGCAGTGTATCTGCTGGAAAAgtgagaatcatggctactcaaatattgcttacctataagatttaatgccctttcatgtgtgtaatctcactgatatgcatcaactgtag
















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|32931087|gb|CF035899.1|CF035899
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13557648|gb|BG549004.1|BG549004
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|32846815|gb|CD986496.1|CD986496
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211157243|gb|FL334276.1|FL334276
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|20803197|gb|BQ294247.1|BQ294247
EST:     ACACACGAGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
EST: gi|32943967|gb|CF048786.1|CF048786
EST:     ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAA                         ATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC
genomic: ACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaattt ... tcatctacagATTTATGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTGCTGGCAAAgtgagaatttttccatcttgatgattattccttgtaagattcattgtttttatgtgtataatctcacagttgttcatctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG