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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactataattgctatgcgattttgatttgttttgaagtttaaacagcatggtgatatacattcttacttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA

Basic information

species Glycine max
transcript GLYMA08G13300.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13300.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------------tactataattgctatgcgattttgatttg--ttttgaagtttaaacagcatggtgata--tacattcttacttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA
                                                        |  | | | | ||   | ||||| ||  |  ||||    ||||    || |  ||  |  |  | | ||  ||     | | | |  |||||||  |||  |||||||| ||||||||||||||||| | ||||||||| ||||| |||||||||||||| | |||||| |||||||| |||||||| || |||||||||  ||
gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA

upper sequence: GLYMA08G13300.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------tactataattgctatgcgattttgatttgttttgaagtttaaacagc-atggtgatatacattc--ttacttgtggaatttttatttttt---gcttgaat-----gccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA
                  | ||  | ||    |||    |    || |  |  |  | |  |||  || |||| || |  |   ||  ||   ||||| | |||| ||    ||||| |       |||||||||||||||||    ||  | ||| | || || || || || ||||| || |  |||  ||| |||||||||||||||||||| |||||||||   |
gtaaacatctggttctgatgctgaagttttcttgcatcgtctgcttttcctagacatcatgcagttattgtgacattccattggttcattcacgaattctgatttgtttgaacttgactcatccaacagGTAGAATTTGATGAAATGGGTCAAGTTATGGGGGTTACTTCCGAGGGGGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATA
















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|8404346|gb|BE059980.1|BE059980
EST:     TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
EST: gi|193688874|gb|FK627851.1|FK627851
EST:     GTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
genomic: GTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
EST: gi|192326977|gb|FK019239.1|FK019239
EST:     TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAGG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
EST: gi|4283991|gb|AI440725.1|AI440725
EST:     TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
EST: gi|24136625|gb|BU927135.1|BU927135
EST:     TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAG                         GTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA
genomic: TTAGTGCTGTTTATGGTGGGACATATATGTTGAATAAGCCTGAGTGCAAGgtatatactc ... tgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatggtgatatacattcttacttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA
               ttcttac  putative branch site (score: 2)
                              tttttattttttgctt  putative PPT
                            aatttttattttttgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactataattgctatgcgattttgatttgttttgaagtttaaacagcatggtgatatacattcttacttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG