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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattcttgttattttgtaggattgattattgaaattttagatgtataaatctaaagatattactggccaatgactaaatagttattgctgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGAGAACAGGAATCATGCCATCTGAGTGGTGAATCTATGGAAACACCTTTAT

Basic information

species Glycine max
transcript GLYMA12G04330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------tgtattcttgttattttgtaggattgattattgaaattttagatgt--ataaatctaaagatattactggccaatgactaaatagttattgct--gtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGAGAACAGGAATCATGCCATCTGAGTGGTGAATCTATGGAAACACCTTTAT
                                                                                           || |  || |      |   | ||| |  || ||    ||       ||  ||   ||   | || |      | | ||  | |||  |   |||||||||||||||| |||||| | |||||||||||    ||   || ||| || |  |||  |||  ||   ||     ||      ||  |||| |  ||| | |
gtataggtttccgaaagtattctactattggatcgaatatgcctttggtgtatattttggcatcatgataatgtctatcaaatagagccagttttccttctcaccctgtgctcattctacaacttccgcatagtggccaaggtacccatgcga-tgtcttgcaccaagattctaattaattgttttttcagGCTGGTGAATTTTTCTATTCAGCTCAAAGAACTGCTGCAGCGCAACAAATGGAAATGGAGGCAAATCAATCTGGTCAAACTTCACTGGAGAGCCCTCTGT
















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|254334717|gb|GR844502.1|GR844502
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|209705919|gb|BW676024.1|BW676024
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|193476826|gb|FK440387.1|FK440387
EST:     CAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGCCGAGCCTTAGAGCAGCAGAGA
genomic: CAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|7685600|gb|AW756248.1|AW756248
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTA-AGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|208275929|gb|GE080271.1|GE080271
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGCCGAGCCTTAGAGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|213617324|gb|DB965195.1|DB965195
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA
EST: gi|208091981|gb|GD890572.1|GD890572
EST:     TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAG                         GCTGGTGAGTTTTTCCACTCAGCTCAAAGCCGAGCCTTAGAGCAGCAGAGA
genomic: TGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTCTGCAGAAGgtacactgcc ... tgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaatctaaagatattactggccaatgactaaatagttattgctgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGAGAACAGGAATCATGCCATCTGAGTGGTGAATCTATGGAAACACCTTTAT
                            gactaaa  putative branch site (score: 2)
                                            ctgtttttc  putative PPT
     atctaaagatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattcttgttattttgtaggattgattattgaaattttagatgtataaatctaaagatattactggccaatgactaaatagttattgctgtttttcagGCTGGTGAGTTTTTCCACTCAGCTCAAAGTCGAGCCTTAGAGCAGCAGAGAGAACAGGAATCATGCCATCTGAGTGGTGAATCTATGGAAACACCTTTAT

tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgac