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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

Basic information

species Glycine max
transcript GLYMA03G42370.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 9
-------------------------atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
                          ||   |    |  |||       | |     |   |       |    ||   |||  | |  | ||| ||  |  | |  | | || | | | | ||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| ||| || |||| || ||||| ||||| ||||||||||| || || || ||
gtaactggaagaactttgaaacttcgttctgggtggtttcttctagatttgtttgttatagtctccacctcaaaagcggataatgctaagctttgttctcacaaactcctgtttgctgt-tacagGAGCTGATATAAGGAGTGTCTGCACAGAAGCTGGCATGTATGCGATTCGCGCCCGACGGAAAACAGTGACTGAGAAGGACTTCCTTGATGCTGTAAACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
---------------atttctgccactccctttcttccctatgacccacgattgaaca--ttgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
                |||| ||       ||   |  ||        | |||||     |||   | |||        || |    ||  |  | |  |||  |   |  |||||||||| |||||||||||||| ||||| ||||| || |||||||| ||||| ||| | ||||| || ||||||||||| || || || || || || |||||
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgttactccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
               |||| ||    ||      | ||    ||| | |     |    |||  | || |   | |    | ||| |||     |||||||||| |||||||||||||||||||| ||||| || ||||| || ||||| ||| | ||||| || |||||||| || || || || || || || || ||
---------gtgtggtttcatctgagtggtttctgctt---tattcgatgacagac---gatcaggttctcacattgccttgcttgttg-----ctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
---------atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
          | ||||     | | || |        || | | |||||   ||  |    ||||   |  |  ||  |||  || | || ||||||       | |||||||||| ||||| || || |||||||||||||| |||||||||||||||||  |||||||||| ||||| ||||| |||||||||||  |||| || ||
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattcttttt--ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 9
atttctgccactccctttcttcccta-tgacccacgatt--gaacat-tgggtagtt-tatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
     ||  ||   || |    || | ||    |  |||  || | | ||  ||  | |||| |  ||     |  ||     ||  |    || | || | |||| || |||||  |||| || || || || || ||||||||||| ||||| ||  | |||||||| |||||||||||||||||| | || || || |||||
-----tggaacattctgtaaagccgagtgttgtagtattttgagcttatgaatacctgtataaaactttaaaatcatgcgcctgaaccaagctgttcctgttcagGTGCGGATATTCGGAGTGTGTGTACGGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAAGACTTCTTGGAAGCTGTCAATAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttc--tctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
                         |   | |  | ||  ||  | | | ||||       |   | |   | ||   | |    |||| ||   |||  ||| || ||||| |||||||||||||||||||| || ||||| || || |||||  | ||||| || ||||| |||||||| ||||| || || || || ||
----------------------gtaagttctcgtgcttatacggtagatggttttctctcctc--tctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 9
atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttc--tctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
                         |   | |  | ||  ||  | | | ||||       |   | |   | ||  || |    |||| ||   |||  ||| || ||||| |||||||||||||||||||| || ||||| || || |||||  | ||||| || ||||| |||||||| ||||| || || || || ||
----------------------gtaagttctcgtgcttatacggtagatggttttctctcctc--tctcggtaaccaagctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA

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|209718785|gb|BW671986.1|BW671986
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|214009507|gb|DB988648.1|DB988648
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|17020809|gb|BM091843.1|BM091843
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|209718786|gb|BW671987.1|BW671987
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|5770628|gb|AI973802.1|AI973802
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGCATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|13482113|gb|BG511456.1|BG511456
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|213600067|gb|DB976026.1|DB976026
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|21595741|gb|BQ610584.1|BQ610584
EST:     CTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: CTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|209702900|gb|BW667435.1|BW667435
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|214007120|gb|DB986168.1|DB986168
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|208066660|gb|GD866417.1|GD866417
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|193429086|gb|FK396344.1|FK396344
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|193350834|gb|FK314156.1|FK314156
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACTG                         GAGCCGATATAAGGAGCGTTTGCA
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCA
EST: gi|193386094|gb|FK352408.1|FK352408
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|193358738|gb|FK328416.1|FK328416
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|213593731|gb|DB971753.1|DB971753
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|214007458|gb|DB987315.1|DB987315
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|208164325|gb|GD961893.1|GD961893
EST:     TTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: TTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
EST: gi|213611119|gb|DB974993.1|DB974993
EST:     AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCG                         GAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG
genomic: AAGGGATATCCGCTTTGAACTTTTAGCTCGGCTTTGCCCAAATTCTACCGgtaagaacac ... ttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA
                       ttttgac  putative branch site (score: 3)
                                     ctttttggttctctcc  putative PPT
                    tttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA