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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagcaagcagaacgatcctgtttgtgattcattattctagactgtttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCGGAGGTGGACGTGGCGCCACTGATGGAGGCGGTGAGCATGAACCCGCGGG

Basic information

species Zea mays
transcript GRMZM5G840582_T03
intron # 2
splice site 3'
intron type U2

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|21391035|gb|BQ529084.1|BQ529084
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|22545220|gb|BU097579.1|BU097579
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|87154658|gb|DY399447.1|DY399447
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21329792|gb|BQ485173.1|BQ485173
EST:     CTCTGACCG-CACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTG-CCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: CTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|71431231|gb|DR812281.1|DR812281
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|71769124|gb|DR967061.1|DR967061
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGA                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21329764|gb|BQ485131.1|BQ485131
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21330631|gb|BQ486012.1|BQ486012
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21329947|gb|BQ485328.1|BQ485328
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21481144|gb|BQ577827.1|BQ577827
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|76011564|gb|DT938734.1|DT938734
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21330897|gb|BQ486278.1|BQ486278
EST:     CAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: CAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21330134|gb|BQ485515.1|BQ485515
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|32869036|gb|CF008718.1|CF008718
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGG--A                         G-G-TGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|76011565|gb|DT938735.1|DT938735
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|26455021|gb|CA826604.1|CA826604
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|50329733|gb|CO524859.1|CO524859
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21480842|gb|BQ577525.1|BQ577525
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|87154082|gb|DY398871.1|DY398871
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21626445|gb|BQ621366.1|BQ621366
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21329951|gb|BQ485332.1|BQ485332
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGG--A                         G-G-TGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21481419|gb|BQ578102.1|BQ578102
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTG-A-------A                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|7216810|gb|AW562932.1|AW562932
EST:     ACTCTGACCGTCGCAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGNCACCTTCAGCAGAGGCGACCCCATGGGAGACGCG
genomic: ACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|5816412|gb|AI987328.1|AI987328
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|78105903|gb|DV524321.1|DV524321
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGA                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21480762|gb|BQ577445.1|BQ577445
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21480818|gb|BQ577501.1|BQ577501
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21480829|gb|BQ577512.1|BQ577512
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGG--A                         G-G-TGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|26455173|gb|CA826756.1|CA826756
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21390418|gb|BQ528467.1|BQ528467
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|71431232|gb|DR812282.1|DR812282
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21329817|gb|BQ485198.1|BQ485198
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|50334092|gb|CO529218.1|CO529218
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|21481478|gb|BQ578161.1|BQ578161
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGC---TG-                         GAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
EST: gi|71434127|gb|DR815177.1|DR815177
EST:     GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGG--A                         G-G-TGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG
genomic: GGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTGGTGAgtgagcagca ... ttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcaagcagaacgatcctgtttgtgattcattattctagactgtttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCGGAGGTGGACGTGGCGCCACTGATGGAGGCGGTGAGCATGAACCCGCGGG
                          attcattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagcaagcagaacgatcctgtttgtgattcattattctagactgtttgcatacagGAGGTGTTCGACAAGGACACCTTCAGCAGAGACGACCCCATGGGAGACGCGGAGGTGGACGTGGCGCCACTGATGGAGGCGGTGAGCATGAACCCGCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG