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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatcaagctaacccattagaattttcgactcttctatttaatttggactgaaggaagttcaaaattgtctttattgcagtagttttcagatgaatcttggttatggtacaaattcctaacaatattgtttactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTTTCAGGTGGATATTGAGAAGAACTGGGTAGAGTCTTGCAAGGTAACTGTT

Basic information

species Glycine max
transcript GLYMA12G30540.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g32570.1 (Oryza sativa), 3'ss of exon 15
gtattatcaagctaacccattagaattttcgactcttctatttaatttggactgaaggaagttcaaaattgtctttattgcag-tagttttcagatgaatcttggttatggtacaaattcctaacaatattgtttactt-------tacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTTTCAGGTGGATATTGAGAAGAACTGGGTAGAGTCTTGCAAGGTAACTGTT
                                                                 | ||| |  | | ||    |  |||     ||||| ||| |||      | ||||  | |  |||  |||  ||       ||||| ||  | || |||| |||||||||||| ||||| || ||||| ||||| |||||  | ||| | |||||||||||||| ||||||| |||| |  || | 
---------------------------------------------------------------gtagattatgctcactgttccttatttatctctgaattttgtttacttggtatattctgatctttatcttttgattccactgctacagAAAGTCTATGAGCAAGCAGGATCTTATTACTGCTCCAACTGACAATCGTTTTCAAATTGATGTCGAGAAGAACTGGGTTGAGTCTTCCAAGATTTCTTTC
















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|208230323|gb|GE032148.1|GE032148
EST:     CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGAT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGAT
EST: gi|193512355|gb|FK468993.1|FK468993
EST:     CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|208104040|gb|GD902225.1|GD902225
EST:     CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|7589119|gb|AW704900.1|AW704900
EST:     CTCTTGTCAAGTTGGCGAAATGCTACATCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCTGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|193324264|gb|FK292628.1|FK292628
EST:     GCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: GCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|193666288|gb|FK610597.1|FK610597
EST:     TCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: TCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|193358097|gb|FK319697.1|FK319697
EST:     CTCTTGTCAAGTTGGCGAAATGCTACATCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCTGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|207714815|gb|GD695033.1|GD695033
EST:     CTCTTGTCAAGTTGGCGAAATGCTACATCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCTGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|207713179|gb|GD697163.1|GD697163
EST:     CTCTTGTCAAGTTGGCGAAACGCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: CTCTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
EST: gi|193331193|gb|FK293269.1|FK293269
EST:     TCTTTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAG                         GAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT
genomic: TC-TTGTCAAGTTGGCGAAATGCTACGTCTGGCTTATGTCCTGTTTGTAGgtattatcaa ... tactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagatgaatcttggttatggtacaaattcctaacaatattgtttactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTTTCAGGTGGATATTGAGAAGAACTGGGTAGAGTCTTGCAAGGTAACTGTT
                             tcctaac  putative branch site (score: 1)
                                           tttacttt  putative PPT
                                    aatattgtttacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatcaagctaacccattagaattttcgactcttctatttaatttggactgaaggaagttcaaaattgtctttattgcagtagttttcagatgaatcttggttatggtacaaattcctaacaatattgtttactttacagGAAAACAATCAGCAGGCAGGATCTTATCACTGCCCCTACTGAGAATCGGTTTCAGGTGGATATTGAGAAGAACTGGGTAGAGTCTTGCAAGGTAACTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC