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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgctattgcctactagcctatactccattcttattcttctgaaccaaatgcatgcgccccgcgcgcgtgctaattgctaacccatgtgctgccat...

Basic information

species Zea mays
transcript GRMZM2G121878_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121878_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g45274.2 (Oryza sativa), 5'ss of exon 4
CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgctattgcctactagcctatactccattcttattcttctgaaccaaatgcatgcgccccgcgcgcgtgctaattgctaacccatgtgctgccat----
||||||||||||||| |||| ||| |||||| |||||||||| ||||||||| ||      | | | |  |   | ||| |   || |||||||    | | |   || |||   |  ||  |||      | ||   |   |  ||||    
CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgctccgtccatttcc---tgctcaaaatttgttcttctttgtctacta-gtgagccaacccagccagctggagttttacggttactcctccatggcc
















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|211236656|gb|FL186528.1|FL186528
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCGTCGGTGACACTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|5525295|gb|AI861134.1|AI861134
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|71428351|gb|DR809401.1|DR809401
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|5525294|gb|AI861133.1|AI861133
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|211236657|gb|FL186529.1|FL186529
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCGTCGGTGACACTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|78117335|gb|DV535722.1|DV535722
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|12968035|gb|BG264982.1|BG264982
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|13178395|gb|BG349668.1|BG349668
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGT
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGT
EST: gi|10697521|gb|BE997245.1|BE997245
EST:     GGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: GGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|13516151|gb|BG518427.1|BG518427
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|78103755|gb|DV522183.1|DV522183
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|211236654|gb|FL186526.1|FL186526
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCGTCGGTGACACTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|74235295|gb|DT643209.1|DT643209
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|6827008|gb|AW330651.1|AW330651
EST:     C-AGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCGTCGGTGACACTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG
EST: gi|211236652|gb|FL186524.1|FL186524
EST:     CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAG                         TACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCGTCGGTGACACTG
genomic: CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgcta ... ctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAAGCCGGAGCTTTTCGGGCCTCTCAAGTCCGGCCAGGCCCCCAAGgtatgcgctattgcctactagcctatactccattcttattcttctgaaccaaatgcatgcgccccgcgcgcgtgctaattgctaacccatgtgctgccat

 AAGAAG
- AGAAGC
- - - -  GGAGCT
- - - - - GAGCTT