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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaagacataaatttgactcaaatgaatcctagtgtattctctaacaaagtaatctcaaatctcaatcttacttctgctgtcttttaatatatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCGAATTTTGAGCAGCGGGCTGAAGCTGTGTTGAGGAAAGTCGTCA

Basic information

species Glycine max
transcript GLYMA08G44410.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 7
------taaagacataaatttgactcaaatgaatcctagtgtattctctaacaaagtaatctcaaatctcaatcttacttctgctgtcttttaatatatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCGAATTTTGAGCAGCGGGCTGAAGCTGTGTTGAGGAAAGTCGTCA
      |    ||  |||   ||    |  || | ||| || ||    |   |||| |     |||  | | |   |         | ||  | | |  || |||| |  |  ||||||||||||||| ||| ||||||   |||||||| |||||| |||| || || |||||||| |||||||| |||||||| ||| ||||||
cacctttgtttactgaaacaggatatcagagagtactaatgaatggcttg--aaagcag----aaaaatgatttccatcctaataattttccacttttcttgtcagAGCTTGGGTGCTGAGAAAGACAGTCTCGACATAGTTCAGCATGAATGGGCCCTACCCAAATTCGAGCAGCGAGCTGAAGCAGTGTTGAGAAAACTCGTCA
















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|193510448|gb|FK470320.1|FK470320
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|31462046|gb|CD404074.1|CD404074
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAAT-TGTGACATAACCCAGCATGACTGGGC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCT-TGACATAACCCAGCATGACTGGGC
EST: gi|9565805|gb|BE475314.1|BE475314
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|207833927|gb|GD808110.1|GD808110
EST:     ATGGGTGGATTTGGTACTTTGATCCTTCAAAG                         GGTCTAAGTGCNGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATGGGTGGATTTGG-A-TTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|10255339|gb|BE823105.1|BE823105
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|208238442|gb|GE042680.1|GE042680
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|192306570|gb|FG997240.1|FG997240
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTTTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|21601342|gb|BQ611673.1|BQ611673
EST:     TTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: TTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
EST: gi|11274440|gb|BF324793.1|BF324793
EST:     ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAG                         GGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC
genomic: ATACACAACGTATGATGCAAATGGGTGGATTTGGATTTGATCCTTCAAAGgtacaaatat ... tatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagtaatctcaaatctcaatcttacttctgctgtcttttaatatatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCGAATTTTGAGCAGCGGGCTGAAGCTGTGTTGAGGAAAGTCGTCA
                                     ttttaat  putative branch site (score: 3)
                                             tatttttc  CT-rich tract
                                 tgtcttttaatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaagacataaatttgactcaaatgaatcctagtgtattctctaacaaagtaatctcaaatctcaatcttacttctgctgtcttttaatatatttttcagGGTCTAAGTGCTGAGAAAGACAATCTTGACATAACCCAGCATGACTGGGCCTTACCGAATTTTGAGCAGCGGGCTGAAGCTGTGTTGAGGAAAGTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - actcaaa
- - - - - - - - - - - - - - - - -tgtattc