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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGGATGCAGAACCAACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaactgacccagagcacagaggcgtttctgtaccatttagcatgctgctttgcttaactatttcaccatgatag

Basic information

species Zea mays
transcript GRMZM2G035636_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035636_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 10
TGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGGATGCAGAACCAACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaactgacccagagcacagaggcgtttctgtaccattta-gcatgctgctttgcttaactatt-tcaccatgatag
|| ||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| |||||| |||||||||||||||||| |||||||  | || |       || | | ||    |   |   |   ||  | | |||||||||| || |||   | | ||
TGGTCCCATGTGCAATGCCTGTGAGATGGCTGTTGTATGGATGCAGAACCAACTTGCACAGAACAAGACTCAGGATCTCATCTTGAACTACATTAATCAGgtgagcttagttaactcctgctctagggccattgtactggtagggatagattttccgttgcttaactgttatcaattttacag
















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|6964727|gb|AW433420.1|AW433420
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCAATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32850229|gb|CD989910.1|CD989910
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|5740635|gb|AI948325.1|AI948325
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32835904|gb|CD975582.1|CD975582
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|33092153|gb|CF052147.1|CF052147
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32850207|gb|CD989888.1|CD989888
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32850559|gb|CD990240.1|CD990240
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|194716945|gb|FK934104.1|FK934104
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|8576947|gb|BE129584.1|BE129584
EST:     AACTTGCCCAGAACAAGACTCAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|7135183|gb|AW497972.1|AW497972
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCAATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32850704|gb|CD990385.1|CD990385
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|211224721|gb|FL222439.1|FL222439
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCAATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... accatgatagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGGATGCAGAACCAACTTGCCCAGAACAAGACGCAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaactgacccagagcacagaggcgtttctgtaccatttagcatgctgctttgcttaactatttcaccatgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA