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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

Basic information

species Zea mays
transcript GRMZM2G134770_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
-----------atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
           |  ||  ||   | ||||| |  ||||||  | ||||||        ||| |  ||   | ||||||||  ||  ||     | ||| || |  ||  |||||||||||  ||||| || ||||||||||| ||| |||||||||||||||||||||| ||||| || ||||| || |||||    || |  || |||||
ccacattgcataagttatgcgtgtcactta-gcactagttcttgtaatggc-------tttgtccttt--ttaattctatataatctttacatctaatatt-tcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA

upper sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 8
atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                   || | |  ||| |    || |   || |||   | || ||| || | |    |   | |||     |  | ||||    ||||| |||||  || || || ||||||||||||||| |||| |  |||||||||||||| ||| |||| || |||||| | |   | ||||| || || ||
------------------gtgagttcttttttaacttgctgctattattggct-ttgcattaactttg---atgctaacat----aattcatttattcagAACAAAAGATGCCTGATGGAAGTTGGAAGTGTGAGAAGTGTAGCAACATAAACTATCCCTTCAGAACCAAGTGCAATAGACAGAACTGTGGGGCCGATAA
















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|32841271|gb|CD980952.1|CD980952
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32839908|gb|CD979589.1|CD979589
EST:     GGATCTAAGTCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGC
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGC
EST: gi|32841323|gb|CD981004.1|CD981004
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32835369|gb|CD975047.1|CD975047
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32840727|gb|CD980408.1|CD980408
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32841497|gb|CD981178.1|CD981178
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                                         tcttatttt  CT-rich tract
                aattctattcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG