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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttattcaaatttcagagttcagtcatcggatttgaagtttggtaatagtggtaatatattacctgaatcctaatcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA

Basic information

species Glycine max
transcript GLYMA15G01680.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 18
tgtttattcaaatttcagagttcagtcatcggatttgaagtttggtaatagtggtaatatattacctgaatcctaatcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
 ||    ||   |||    |||||    |  |   |   | ||| ||||        |    | ||  |||  | || |  |||     ||   | | |||||||| ||||||||||||||||| || ||| | || || || |||||  |||| ||||||||| | ||||||||||||||  |  | ||||||||||  
-gtgccatcctgtttgtctgttcaaaattttg---tagtggttgttaatttaaacttttatgtgccccaatgtttat-atgatttacttttggcttgcagTGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATATAGCCACTGACCCTAATTACAGATTTGATCTGGCTGTGCAGCTTGGAAGC

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
------------------------------------------------tgtt--tattcaaatttcagagttcagtcatcggatttgaa-gtttggtaatagtggtaatatattac----ctgaatcctaa--tcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
                                                ||||  ||  ||  | ||  || |||   |  || ||  |  ||||    | | |       |  |||    |||| ||   |  ||||||| ||     || ||  || ||||| || ||  | || ||||| || |||| |||||||||||| |||||||| ||||| ||||| |||||||||||  |  | |||||||| || | |
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 17
----tgtttattcaaatttcagagttcagtcatcggatttgaagtttggtaatagtggtaatatattacctgaatcctaatcaaa--attcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
    |  | | || | ||    |    |||   |  |  |     | |||  |   |   | |  |  | | | |  |  ||  |  ||| | || ||   | |||||| ||||||||| | || ||||| || ||||| ||||||||||| ||| | || || || ||||| |||||||||||  |  | ||||| || || | |
gatctactgactcta-ttgtttaacatagttg-cacacctatcaatgggtgttt-cgtggacaactctctttatttattttcggacaattttcgactt---gttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
tgtttattcaaatttcagagttcagtcatcg-gatttgaagtttggtaatagtgg----taatatattacctgaatcctaatcaaaattcttgattttatgg-tagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
      |   || ||       |  | |    ||    ||| |   | ||  ||     |  ||  || | || || ||||| | ||   ||| ||  || | ||||||||||| |||| | |||||||| || |||||||| ||||| || |||||||||||||||||||| ||| ||||||| ||| |||| |||||||| | |
------tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA

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|208274876|gb|GE068494.1|GE068494
EST:     GAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAG                         TGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAG
genomic: GAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagtta ... tttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAG
EST: gi|208327786|gb|GE124604.1|GE124604
EST:     GAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAG                         TGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGT
genomic: GAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagtta ... tttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatagtggtaatatattacctgaatcctaatcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
                            taatcaaaattcttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttattcaaatttcagagttcagtcatcggatttgaagtttggtaatagtggtaatatattacctgaatcctaatcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA

- - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa