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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgactattttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC

Basic information

species Glycine max
transcript GLYMA08G16770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgactattttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC
                                                               || |||| |   ||||||| |  |     | | || | |      ||   ||   | ||| ||        |  | ||| || | | | ||   ||    ||||||| || ||||| |||||||| ||||||||||| |||||||   | ||    |||    |||| |  ||||| |||||||||  | | ||||||||||
------------------------------------------------------------gtatggttataa---ttttgatcacatagataattttcaggtcagatcttgaattagaattatata--------acatatgatattatctt-ttgtatc----agGGAATACGGTTTAGAGGCATGTCGATTCCTGAATGTCAGAAAATATTACCTTCAGCTGAGTCTGGAGAAGAGCCCTTGCCTGAGAGTCTTCTGTGGCTTC

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 6
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgctt--atgactattttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC
     |||||   |    |   |  || |   |  ||||| |       | |   |||  | ||  ||  |||||| ||| ||| ||| | | | |  |  |       |||| ||| ||  |   |    |||  |  ||||| |   | |  ||  || ||  ||||||||||||||||||| ||||| || ||||||||||| |||    | |||  |||    |||||||| |||||| ||||||||| | | || |||||||
----gtaaatatcccttttaacccattcttgaaactttgttat----ggattcttttatattttattttaatgactgttt-gatgaat-gttgggacatgagggaagatttttatttttttttgggtttccaatttagttctgaaagttg-agcttctgtttttcagGGAATTCGCTTTAGGGGTATGTCTATCCCTGAATGCCAAAAAGTATTACCAAATGCAACACCTGGTGGAGAGCCTCTGCCTGAGGGTCTGCTTTGGCTTC

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 5
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgacta--ttttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC
                                                            | || |  |  | ||  |  ||   |  | || |    |  |   |    |  |  ||    | |   | ||||   |      |||| | ||  | | | ||  |||| |||||||| || |||||||||||||||||||| ||||||||||||||||  ||| | |||||||| || ||  | || || |   |  ||||||| |
---------------------------------------------------------ggttttttcccaaaagtagatcctgggaagctaatgg----ttgggcattttgtaggactgagcgtttcacccgaataatt------gatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC

upper sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S56_197V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgactattttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtctt--atagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC
                            | ||   | | |  |     ||   | |||| | |||    ||| ||||   ||   |  ||  | | | |     |     | |    ||| ||  | ||||||     ||    | | |||   |  | ||   ||||  |||||||| || ||||||||||| |||||||| |||||||| |||||||  |     ||||||||  | || |||||||| |   |  ||||||| |
---------------------------gtgagtgctatatatcctgtgaa---agttaagtgttg----tgattattcatatgtttaaatccactgtttagcacaatacat-tagagtaacatacaatgaatg-----ctatatttaacatacaattttttccgtagGATATTCGCTTCAGAGGCATGTCAATACCTGAATGTCAGAAAAAACTTCCAGAAGTGAAACCTGGTGGCAAACCATTGCCTGAAGGCTTTTTGTGGCTCC

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|213593279|gb|DB966104.1|DB966104
EST:     GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG                         GGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
genomic: GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAGgtatataaat ... cgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
EST: gi|14206066|gb|BG839744.1|BG839744
EST:     GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG                         GGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
genomic: GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAGgtatataaat ... cgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
EST: gi|13562412|gb|BG550632.1|BG550632
EST:     GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG                         GGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
genomic: GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAGgtatataaat ... cgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
EST: gi|209725513|gb|BW677810.1|BW677810
EST:     GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG                         GGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA
genomic: GAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAGgtatataaat ... cgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC
    tgttaat  putative branch site (score: 3)
      ttaatatttactgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgactattttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG