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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatgtattttgtgtgtatatatatgctttgtttccttctaggttaatttgtccatttgagtaatgagaagtttttcatttttcccactatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG

Basic information

species Glycine max
transcript GLYMA11G19660.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G08190.1 (Arabidopsis thaliana), 3'ss of exon 7
aagatgtattttgtgtgtatatatatgctttgtttccttctaggttaatttgtccatttgagtaatgagaagtttttcatttttccc---actatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG
   ||     | |    | | | |  |         ||  || |||   || ||  |||     || |    ||||  ||| |  |    || |  | |  |||||||| || |||| ||||||||| |||||||||||||||||||   |||||| |||||||| || ||||| ||| | |||||||| |||||||| ||||
ttcataagcctggaaaatct-tgttcgagaaaccaactgttaagttctcttttc--tttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG

upper sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0061g00940.t01 (Vitis vinifera), 3'ss of exon 7
aagatgtattttgtgtgtatatatatgctttgtttccttctaggttaatttgtccatttgagtaatgagaagtttttcatttttcccactatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG
| |   || |   |   ||| |  ||      |||   | |||  |  ||  |  |||  |  |  ||| |   |||||| ||  || |||| |    |||||||||| || ||||| || ||| ||||||||||||| |||||   |||||| |||||||||||||| || ||| | || ||||| |||||||||||||
agggcttaataattccatattttgatttccaatttttgtttagactgtttaatatattcaataacagagtatgctttcatcttgtcctctatatgcatagGTGGGATCAAGATACCTGGACCATTTGATTGTGGAAAGGAAATATGCTGAAGCTGCATCTTTGTGTCCTAAATTGTTGCGTGGATCTGCTTCAGCATGGG
















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|6502313|gb|AW203686.1|AW203686
EST:     CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAG                         GTGGGATCTANGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
genomic: CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAGgtatttaagt ... atctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
EST: gi|10237520|gb|BE806408.1|BE806408
EST:     CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAG                         GTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
genomic: CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAGgtatttaagt ... atctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
EST: gi|7693152|gb|AW761249.1|AW761249
EST:     CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAG                         GTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAAGAAAATACAGTGA
genomic: CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAGgtatttaagt ... atctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGG-AAAGAAAATACAGTGA
EST: gi|151399580|gb|EV269451.1|EV269451
EST:     CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAG                         GTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
genomic: CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAGgtatttaagt ... atctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
EST: gi|17518655|gb|BM187697.1|BM187697
EST:     CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAG                         GTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA
genomic: CTTTGGCTGTGGTTGAATCTGGTCAGGGACGGAGTGAACTACTTGATGAGgtatttaagt ... atctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttgtccatttgagtaatgagaagtttttcatttttcccactatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG
 ggttaat  putative branch site (score: 4)
                           tttttcatttttccca  putative PPT
                        aagtttttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatgtattttgtgtgtatatatatgctttgtttccttctaggttaatttgtccatttgagtaatgagaagtttttcatttttcccactatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT