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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgttttcaactgaatgataaatttgacgcgttggcttgtcgcatgtgcacttcagtcctgttatttgagtcaataatcatcacatcgtttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGCTTAGAGACAAG

Basic information

species Zea mays
transcript GRMZM2G157332_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157332_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 5
--atcgttttcaactgaatgataaatttgacgcgttggcttgtcgcatgtgcacttcagtcctgttatttgagtcaataatcatcacatcgtttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGCTTAGAGACAAG
   ||   |   ||||        |||| |  | ||    |||| | |    ||||  |      ||||||  |  | |    | ||||| ||| || | |||||||||||| ||| | ||||| || ||||||||||| |||||||  ||||||||||| || 
atttccactggcactggtcttgttatttcattcctttctctgtctctttgttacttgtgattacatatttgtttttacagct-taacatcttttgctac-agCTGAAAGAGAAGCTGTGAGTGCAGCAGAAAAGGCAGAGAGAAAGGTGCAGCTTAGAGATAAA
















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|211008698|gb|FL168938.1|FL168938
EST:     TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG                         CTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
genomic: TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGGgtatgtcaca ... ttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
EST: gi|148929096|gb|EC874464.2|EC874464
EST:     TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG                         CTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
genomic: TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGGgtatgtcaca ... ttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
EST: gi|16378394|gb|BI992425.1|BI992425
EST:     TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGG                         CTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
genomic: TGTGAACCGCTTGAATAAGACAAAGGTGGAACGGAAACCTGATTTAAAGGgtatgtcaca ... ttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
EST: gi|13559010|gb|BG550365.1|BG550365
EST:     AAAGGTGGAACGGAAACCTGATTTAAAGG                         CTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC
genomic: AAAGGTGGAACGGAAACCTGATTTAAAGGgtatgtcaca ... ttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcacttcagtcctgttatttgagtcaataatcatcacatcgtttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGCTTAGAGACAAG
                                         tcgtttcct  CT-rich tract
                            aataatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgttttcaactgaatgataaatttgacgcgttggcttgtcgcatgtgcacttcagtcctgttatttgagtcaataatcatcacatcgtttcctgccagCTGAAAGAGAGGCTATTAGTGCTGCTGAAAAGGCAGAAAGAAAGGCACAGCTTAGAGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA