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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtccaattgttgttttgtttttttggtgtgtgcacactactgtataacattagtattgctttcgtgatctctgctgacatgttccttttccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG

Basic information

species Zea mays
transcript GRMZM2G174696_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 1
ggtccaattgt-tgttttgtttttttggtgtgtgcacactactgtataacattagtattgctttcgtg-atctctgctgacatgtt-----ccttttccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG
       ||||  | |||| | | ||| ||  | ||  ||| | | || |   | | | ||| | |   || |||  ||  |  ||     | || ||| ||| ||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| || || ||||||||
-------ttgtgcgatttgatctgttgttgcatacatgctattttctatctgaattttggctcttgaacatttcttttgtgagtttgctgacattctccattttcagTGTCGTTGAAACCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACTAAAGGATTAAATCAGAAGTTCTCACTCAGCCACAG
















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|211089741|gb|FL262759.1|FL262759
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGATTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|31353843|gb|CD438200.1|CD438200
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGATTTGTCTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|51593036|gb|CV072182.1|CV072182
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGATTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|211087304|gb|FL262757.1|FL262757
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|211089744|gb|FL262762.1|FL262762
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGATTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|5268993|gb|AI770957.1|AI770957
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|211402157|gb|FL346436.1|FL346436
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|149090165|gb|EE179465.2|EE179465
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|211210889|gb|FL339225.1|FL339225
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAA
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAA
EST: gi|211089743|gb|FL262761.1|FL262761
EST:     CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGA
genomic: CAACCTCCCCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttacagTGTCTTTGAAGCCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacattagtattgctttcgtgatctctgctgacatgttccttttccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG
                           tgctgac  putative branch site (score: 2)
                                 catgttccttttcctt  CT-rich tract
     ttagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtccaattgttgttttgtttttttggtgtgtgcacactactgtataacattagtattgctttcgtgatctctgctgacatgttccttttccttttacagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - tgttgtt
- - - - - - - - tgttttt
- - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - actactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgctg