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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaagtttattatgaaaatctactttgtactttgtttatctacccacctgtcttcatctggccttgctgttctcatatgttagtctgttttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAACATAACTGTGGATATG

Basic information

species Zea mays
transcript GRMZM2G063851_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 3
ataaaagtttattatgaaaatctactttgtactttgtttatctacccacctgtcttca----tctggccttgctgttctcatatgttagtctgttttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAACATAACTGTGGATATG
     || | |  |    | | |    |  ||| | | |||   |  |  |    |||    || ||             |     |   |  || || ||||||||||||||||||| || || ||||| ||||| |||  ||||||||||||||||||||| ||||||
----tagctcaccagttcacttttacctaaactctatatatgagctgatttcctgtcaaagatcaggatagaaaagcacaactcactttaccattctggtacagGATCGCTTAAAGAAACTTAAATCAGAACATGGGAAGGTCCAGCTTGGAAACATAACTGTTGATATG

upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 4
ataaaagtttattatgaaaatctactttgtactttgtttat-ctacccacctgtctt-catctggccttgctgttctcatatgttagtctgttttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAACATAACTGTGGATATG
  |   |  |    ||    |   ||      |       | | |    ||||||    | | ||             |     |   |  || |||||||||| ||||||||||| || || || ||||||||||||  ||| |||||||| ||||| || ||||||
--agttgcatgccctgtgctttgtctcaaccatccaagagtgccaaattcctgtcaaataccaggaaagaaaagctcaactcactttaccattctgttacagGACCGCTTAAAGAAACTTAAATCGGAGCATGGAAAGGTCCAACTTGGAAATATAACAGTCGATATG
















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|211505526|gb|FL228165.1|FL228165
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507876|gb|FL228171.1|FL228171
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507874|gb|FL228169.1|FL228169
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211059244|gb|FL131321.1|FL131321
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|148932412|gb|EC876097.2|EC876097
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507879|gb|FL228174.1|FL228174
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|93284646|gb|EB676910.1|EB676910
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211510249|gb|FL228196.1|FL228196
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|148974563|gb|EE025351.2|EE025351
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211510246|gb|FL228193.1|FL228193
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507880|gb|FL228175.1|FL228175
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507878|gb|FL228173.1|FL228173
EST:     GATCTTAAGTCCCCAGTTGCAGGAATTGATTCCCGGAACAACAG                         GATCGCTTAAAGAAGCCTCAAGTCAGAGCATGGAAAGACCCCAGCTTGGAA
genomic: GATCTTAAGTCCC-AGTTGCAGGAATTGATTCC-GGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGC-TCAAGTCAGAGCATGGAAAGACCC-AGCTTGGAA
EST: gi|211510237|gb|FL228184.1|FL228184
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507873|gb|FL228168.1|FL228168
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507884|gb|FL228179.1|FL228179
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211507875|gb|FL228170.1|FL228170
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC
EST: gi|211505527|gb|FL228166.1|FL228166
EST:     GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG                         GATCGCTTAAAGAAGCTCAAGTCTGAGCATGGAAAGACCCAGCTTGGAAAC
genomic: GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAGgtttgctgcg ... tttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacctgtcttcatctggccttgctgttctcatatgttagtctgttttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAACATAACTGTGGATATG
                                        tctgtttt  CT-rich tract
                               atatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaagtttattatgaaaatctactttgtactttgtttatctacccacctgtcttcatctggccttgctgttctcatatgttagtctgttttgttacagGATCGCTTAAAGAAGCTCAAGTCAGAGCATGGAAAGACCCAGCTTGGAAACATAACTGTGGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA