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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTCGATCCCGCTCAGCCAGGCGGCAGAGGCTGTCGACCCCGAGGACCCGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatctagtctctacgctccttcgtttgcttcgtgagttgcggcggcattggactagttgcgcgcctgtgctgcccttttagggtcttgctgaccg...

Basic information

species Zea mays
transcript GRMZM2G149662_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 1
GACGTCGATCCCGCTCAGCCAGGCGGCAGAGGCTGTCGACCCCGAGGACCCGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatctagtctctacgctcc-----ttcgtt------tgcttcgtg---agttgcggcggcattgga---ctagttgcgcgcctgtgctgcccttttagggtcttgctgaccg
 |||||||||||||||||||||||||| ||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||||  | |  |   ||      ||||        || ||| |   ||  ||||| |||||||    ||| | ||||||| ||||||| | |                  
AACGTCGATCCCGCTCAGCCAGGCGGCGGAGGCGGTTGACCCGGAGGACCCGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACCCGCAAGgtctggatctaacccccccaacccacgcgctcgtcgtgctgcgcctcgcggcgaggggcggctgcattggggggctaatcgcgcgcccgtgctgctcctg-----------------
















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|211293666|gb|FL114590.1|FL114590
EST:     CGGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|149096821|gb|EE182610.2|EE182610
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|78081652|gb|DV510064.1|DV510064
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|50323915|gb|CO519041.1|CO519041
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|76288284|gb|DV027852.1|DV027852
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|91053026|gb|EB163444.1|EB163444
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|148956825|gb|EC902729.2|EC902729
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|149109464|gb|EE190213.2|EE190213
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|5325136|gb|AI783327.1|AI783327
EST:     CCCA-CTCGCCCACCACCTCCACACGC-AG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|71771810|gb|DR969747.1|DR969747
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|211293665|gb|FL114589.1|FL114589
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|74034904|gb|DT535394.1|DT535394
EST:     CGGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|5901280|gb|AW042380.1|AW042380
EST:     CCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|88756505|gb|DY540646.1|DY540646
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|32862594|gb|CF002276.1|CF002276
EST:     CGGCCAAGTCGCCGCCGCGACCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|71440103|gb|DR821153.1|DR821153
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|50331144|gb|CO526270.1|CO526270
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|78077279|gb|DV505713.1|DV505713
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCCAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|71772305|gb|DR970241.1|DR970241
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
EST: gi|71446982|gb|DR828032.1|DR828032
EST:     CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAG                         GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA
genomic: CGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatct ... ttctgtgcagGCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAGTTTATGACTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTCGATCCCGCTCAGCCAGGCGGCAGAGGCTGTCGACCCCGAGGACCCGGCCAAGTCGCCGCCGCGGCCCAGCTCGCCCACCACCTCCACACGCAAGgtccggatctagtctctacgctccttcgtttgcttcgtgagttgcggcggcattggactagttgcgcgcctgtgctgcccttttagggtcttgctgaccg

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