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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTGAGAGGCCCCGCCGCCGCTCTGCGTAGGAGCACGGTGCGCCGCCGTGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctgtaccgccagatatcctgaaaatagttgcatttgtcgcgtgtgatcaattacgatgctgcattggatgtgaccaaccgtattgttttgaat...

Basic information

species Zea mays
transcript GRMZM2G081642_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081642_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 5'ss of exon 1
GCGCTGAGAGGCCCCGCCGCCGCTCTGCGTAGGAGCACGGTGCGC-CGCCGTGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctgtaccgccagatatcctgaaaatagttgcatttgtcgcgtgtgatcaattacgatgctgcattgg-atgtgaccaaccgtattgttttgaat-----------
  |  |||       |  |  ||  ||   | |   | |   |   ||||||| | ||||||||| ||||||||||| ||||||||||||||||||||||||||| | |  | ||| |      |||     |  ||||  |||| | |||   |       | || | |||||| ||||| ||   |||| |||| |||||           
AGGAGGAGGAATTGGGGGGAGGCCGTGGCGACGCCTAGGTCCCTTGCGCCGTG-GACGCCATGATTGAGCAGTTCGTCAATTTCGTCATCCGGCCGCCCCGgtacccac-attccgtcg----ccct-----tgtttgc--ttgtggtgtgaatttggcatggttggtacattggcatgtggccgtacgtactgttgtgaattgggagatttg
















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|211317674|gb|FL189179.1|FL189179
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|26455576|gb|CA827159.1|CA827159
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|37424864|gb|CF650166.1|CF650166
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|21481543|gb|BQ578226.1|BQ578226
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|148941968|gb|EC886955.2|EC886955
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|71436402|gb|DR817452.1|DR817452
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|149069709|gb|EE158095.2|EE158095
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|101394355|gb|EB819112.1|EB819112
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|149041290|gb|EE046926.2|EE046926
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCTTGC
EST: gi|213187018|gb|FM194143.1|FM194143
EST:     TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCG                         GTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCCNNNG
genomic: TGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctg ... taatttgcagGTCAGAATATAATCCAGATCAGTATCTATGGGAGAAAGAGTTTATCC-TTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCTGAGAGGCCCCGCCGCCGCTCTGCGTAGGAGCACGGTGCGCCGCCGTGAGGCGCCATGATCGAGCAGTTCGTTAATTTCGTCATCCGGCCGCCCCGgtacgcgctgtaccgccagatatcctgaaaatagttgcatttgtcgcgtgtgatcaattacgatgctgcattggatgtgaccaaccgtattgttttgaat

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