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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACCTGCCCCCTGCGCCGTCGGGATGTACGTGCCGCCGCCGCCCACCGGCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatctctacctgccaccctccttttctctccccatctggccgcagtggtccgtgcgacgttgatgggattgtaactgctgatttcgccccgtac...

Basic information

species Zea mays
transcript GRMZM2G068657_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068657_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 1
--GCCACCTGCCCCCTGCGCCGTCGGGATGTACGTGCCGCCGCCGCCCACCGGCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatctctacctgccaccctccttttctctccccatc----tggccgcagtggtccgtgcgacgttgatgggattgtaactgctgatttcgccccgtac
  ||  |  |      | ||||  |  || | ||  |||  || |||  ||| || ||||||||| |||||||||||||||||||| |||||||||||||||||||| | |||||  ||  | | |||  |  ||||| |  ||    | ||||||| |    |   ||  | |||  |    || | ||  | |  || |     
CGGCGGCGGGATGTACGTGCCGCAGCCATCT-CGCTCCGATGCGGCCGGCCG-CGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactctctctctctctctctctctccctctctctctcgcctttgccgcagggtgaagctggagctggatctgtacttagcggcgcactatgcgca----
















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|148966165|gb|EE017106.2|EE017106
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|148990972|gb|EE032403.2|EE032403
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|71325398|gb|DR799378.1|DR799378
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|101385920|gb|EB815008.1|EB815008
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|78115179|gb|DV533567.1|DV533567
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|88752220|gb|DY536361.1|DY536361
EST:     CGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: CGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTC-TGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|71325717|gb|DR799546.1|DR799546
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|148978876|gb|EE026371.2|EE026371
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
EST: gi|148960850|gb|EE011526.2|EE011526
EST:     GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAAC                         GAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG
genomic: GCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatc ... ccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACCTGCCCCCTGCGCCGTCGGGATGTACGTGCCGCCGCCGCCCACCGGCGGCGCCGGCGAGCAGCCTAGGGTTTACCAGGTCTGGCGGGGAAGCAACgtaaggaatctctacctgccaccctccttttctctccccatctggccgcagtggtccgtgcgacgttgatgggattgtaactgctgatttcgccccgtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA