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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgttgtttccttttgttaccccttcagagctattgttttgagcaacctgggcctactttttgttttataaaagatattattatggcgtatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGACAAGGATGCTGGGATGACACGGCTTAACCTATTCTCACCTTGCAAA

Basic information

species Zea mays
transcript GRMZM5G859195_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g58790.2 (Oryza sativa), 3'ss of exon 1
--gtttgttgtttccttttgttaccccttcagagctattgttttgagcaacctgggcctactttttgttttataaa-agata--ttattatggcgtatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGACAAGGATGCTGGGATGACACGGCTTAACCTATTCTCACCTTGCAAA
   |   || | |  | |||  | |   | | |   ||| || |||  |  |     ||  |  |      ||||  | |||  |||| |||| || |  |||||||    ||||| | |||||| | ||| ||| || |||| |||||||||||| || |||||||||| |||||||| |||||||||||||||||||||
ttataaattctgttttcttgggagcttctaaaa---attcttctga--agtccttttcttttcctgacacaataagtatatagtttataatggtgtgtactttagGTTGAGTATGATCTACAAGCAAAGTTCAACAAGCTAGCGGACCAAATTGACCAGAATGCTGGGATTACACGGCTGAACCTATTCTCACCTTGCAAA
















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|211042887|gb|FL185937.1|FL185937
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042886|gb|FL185936.1|FL185936
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAATGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211337627|gb|FL219918.1|FL219918
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|71768978|gb|DR966915.1|DR966915
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042883|gb|FL185933.1|FL185933
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|148969055|gb|EE019774.2|EE019774
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|148955559|gb|EC901197.2|EC901197
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|76021627|gb|DT948797.1|DT948797
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|149103617|gb|EE289017.2|EE289017
EST:     TCAGCCTGAGAGTCCCCGCGTCATTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCACACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|91870954|gb|EB401166.1|EB401166
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042884|gb|FL185934.1|FL185934
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCNAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042881|gb|FL185931.1|FL185931
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGKAATGAGGCAAKTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042882|gb|FL185932.1|FL185932
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|149080472|gb|EE169502.2|EE169502
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042885|gb|FL185935.1|FL185935
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAANTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|13198608|gb|BG354410.1|BG354410
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211337629|gb|FL219920.1|FL219920
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
EST: gi|211042888|gb|FL185938.1|FL185938
EST:     TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAG                         GTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC
genomic: TCAGCCTGAGAGTCGCCGCGTCGTTCGAGCAGGGAAGGAGGCAAGTGGAGgtaagcgcct ... tatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctgggcctactttttgttttataaaagatattattatggcgtatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGACAAGGATGCTGGGATGACACGGCTTAACCTATTCTCACCTTGCAAA
           tactttttgttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgtttccttttgttaccccttcagagctattgttttgagcaacctgggcctactttttgttttataaaagatattattatggcgtatgttttagGTCTCTTATGACCCACAAGCGAGGTTTAACCAGATAGCAGACCAAATTGACAAGGATGCTGGGATGACACGGCTTAACCTATTCTCACCTTGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- -tgttgtt
- - - - - - -ttttgtt
- - - - - - - - - - - cccttca
- - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagata