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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaatcttttagattattatttattcgcattttttatgatttatcttttttatgtagtgatttttgtcaccaatatgtttgcttttgatgtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAACAAAAAAGAGGCAAAATTTTATGGAAATATGTTCAACAAACTGCACAAG

Basic information

species Glycine max
transcript GLYMA03G21690.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------------ttaaatcttttagattattatttatt---cgcattttttatgatttatctttt--ttatgtagtgatttttgtc----accaatatgtttgcttttgatgtat-----aaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAACAAAAAAGAGGCAAAATTTTATGGAAATATGTTCAACAAACTGCACAAG
                                                          ||||    |   ||||  ||  | |    | | || | |  |  | ||  ||  | | |||||   |     |       |  ||  |  || || |||| |     |||||||||||| ||||| ||||| |  ||||| |||||||| |||||||||||||| || |||||||| ||||| ||||| || |||||    |   || |||||
gtatcagattatatcttgcctcttgatctgatttccaatgtgacgaacttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacagGGATGTAAAGCTGGAGTATAGAACTTTAAAGGAAAAAATGAAGGAGTACAATAAGAAAGAGGCCAAATTCTATGGCAACATGTTTGCAAGGATGAACAAG

upper sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------ttaaatcttttagattattatttatt---cgcattttttatgatttatctttt--ttatgtagtgatttttgtc----accaatatgtttgcttttgatgtat-----aaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAACAAAAAAGAGGCAAAATTTTATGGAAATATGTTCAACAAACTGCACAAG
                                                          ||||    |   ||||  ||  | |    | | || | |  |  | ||  ||  | | |||||   |     |       |  ||  |  || || |||| |     |||||||||||| ||||| ||||| |  ||||| |||||||| |||||||||||||| || |||||||| ||||| ||||| || |||||    |   || |||||
gtatcagattatatcttgcctcttgatctgatttccaatgtgacgaatttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacagGGATGTAAAGCTGGAGTATAGAACTTTAAAGGAAAAAATGAAGGAGTACAATAAGAAAGAGGCCAAATTCTATGGCAACATGTTTGCAAGGATGAACAAG
















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|7285868|gb|AW598355.1|AW598355
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|57574028|gb|CX547003.1|CX547003
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|58014983|gb|CX701725.1|CX701725
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|192333549|gb|FK026850.1|FK026850
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|9900273|gb|BE609241.1|BE609241
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAANAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|192316141|gb|FK011584.1|FK011584
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|192319168|gb|FK009108.1|FK009108
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|6666583|gb|AW278042.1|AW278042
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|9900283|gb|BE609251.1|BE609251
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGANGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|193508335|gb|FK466178.1|FK466178
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|57574341|gb|CX547316.1|CX547316
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|192316140|gb|FK011583.1|FK011583
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
EST: gi|10254863|gb|BE822629.1|BE822629
EST:     TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAG                         GGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA
genomic: TTGGCCGAATTTGATATTAAGAAAGCGCTTGAGATTGACCCTAACAACAGgtggattata ... gtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttatgtagtgatttttgtcaccaatatgtttgcttttgatgtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAACAAAAAAGAGGCAAAATTTTATGGAAATATGTTCAACAAACTGCACAAG
                                      ttttgat  putative branch site (score: 4)
                                      ttttgatgtataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaatcttttagattattatttattcgcattttttatgatttatcttttttatgtagtgatttttgtcaccaatatgtttgcttttgatgtataaacagGGATGTCAAGCTTGAGTACAAGACTTTGAAGGAAAAGATGAAGGAGTACAACAAAAAAGAGGCAAAATTTTATGGAAATATGTTCAACAAACTGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc