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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcacttagcactggaaaatggatatatttcaagagctgtggaatactttacatttacgtatctgctgctatttacctttttttttggtttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCT

Basic information

species Glycine max
transcript GLYMA08G22580.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22580.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 3
tttcacttagcactggaaaatggatatatttcaagagctgtggaatactttacatttacgtatctgctgct--------atttaccttttttt--ttggtttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCT
           | ||| |  |  || |||  || ||| ||| ||    || | |||   |   |   ||||        | |||||||||| |  ||| ||| | |  |||| | |||||||||||||| |||| |||| ||||||| ||||| ||||||||||| |||| ||||||||| |||||||| ||||| ||||  || ||  |
---------agaatggcactttcatttatagca-gagttgttgaccttttaagattcttgatcccattgctgattttttaattacctttttctggttgatttctttgaagTGGCAGAAGTGATCTTTGTTATAATCTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTT
















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|22933051|gb|BU550190.1|BU550190
EST:     CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|15815415|gb|BI787690.1|BI787690
EST:     CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|208112989|gb|GD910628.1|GD910628
EST:     GATGTTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: GATG-TCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|254314950|gb|GR829943.1|GR829943
EST:     GACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: GACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|20813268|gb|BQ297746.1|BQ297746
EST:     GTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: GTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|41146511|gb|CK606722.1|CK606722
EST:     CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|208230035|gb|GE023390.1|GE023390
EST:     CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
EST: gi|208263701|gb|GE062869.1|GE062869
EST:     CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCT                         TGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA
genomic: CGATGTCAGCATCTATGTCGTGGGCAAGGATGAGTATGACGAACTTGCCTgtatgtattt ... ttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttacatttacgtatctgctgctatttacctttttttttggtttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCT
                        ctatttaccttttttt  CT-rich tract
                         tatttacctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcacttagcactggaaaatggatatatttcaagagctgtggaatactttacatttacgtatctgctgctatttacctttttttttggtttttctctagTGTCCGAAGTGATCTTTGTGATAACCTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - cactgga
- - - - - - - - - - - - - - - - - - gctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatctg