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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcacaattatgtgcaaatgcagaaattaactgcgtttcgatgagtttaagtgttgtaaaaatttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA

Basic information

species Glycine max
transcript GLYMA08G02940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 1
agcac-aattatgtgcaaatgcagaaattaactgcgtttcgatgagtttaagtgttgtaaaa-atttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA
  ||  |||||| |||   || | |  |   |       |||| | |       |  || || || || ||     |||  || ||     | | |    |||||  || |||||  ||||  |||| ||||||||  |||  ||| | || || || ||||| ||||||||||| |||||||| || ||||||||||| ||
-acatgaattatatgcctgtgtatatgtgtgccaatacacgataaatggtgaattgatagaacatgtagcttacatactgccactgctcc-tctgtttgcagGATCCCTGTTTGCATTTTCTGTTGCGAAGGAGGAGACCAAGAAGCTCGGTACCGTGATCGGTATTGATCTTGGTACAACCTACTCGTGTGTCGGTGTGTA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 1
----agcacaattatgtgcaaatgcagaaattaactgcgtttcgatgagtttaagtgttgtaaaaatttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA
    || ||    | |    |   |   || | |    | ||| | | | |     | |||   |  || | |       ||| |||   ||| |       ||||| ||||  ||| ||||||||||| || |||||||| |||||||| || || |||||||| || ||||||||||||||||| |||||||| ||||||||
agaaagaactgacaagctggatcacctgaactgaaaatggttctaagtgctg----gctgtgtgagctttatttgagtcttaatatttccaaactgtattgcagGATTTCTAGCTGCAATTTCCATTGCAAAAGAGGAAGCAACCAAGTTGGGAACTGTCATCGGGATAGATCTTGGAACAACCTACTCATGTGTTGGTGTTTA
















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|254343099|gb|GR859261.1|GR859261
EST:     TGGCTCGTGGGCACGCCGTTCTCTGATTGTTCTAGCCATCATTTCCTTCG                         GATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA
genomic: TGGCTCGTGGGCACGCCGTTCTCTGATTGTTCTAGCCATCATTTCCTTCGgtaatttcac ... ttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA
EST: gi|254341733|gb|GR852870.1|GR852870
EST:     TGGCTCGTGGGCACGCCGTTCTCTGATTGTTCTAGCCATCATTTCCTTCG                         GATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA
genomic: TGGCTCGTGGGCACGCCGTTCTCTGATTGTTCTAGCCATCATTTCCTTCGgtaatttcac ... ttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA
EST: gi|193691995|gb|FK631034.1|FK631034
EST:     TTGTTCTAGCCATCATTTCCTTCG                         GATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA
genomic: TTGTTCTAGCCATCATTTCCTTCGgtaatttcac ... ttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtgttgtaaaaatttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA
                            aactaac  putative branch site (score: 1)
                                            tttctccat  putative PPT
           taaaaatttaactatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcacaattatgtgcaaatgcagaaattaactgcgtttcgatgagtttaagtgttgtaaaaatttaactatgtaactaacattgagaaatttctccatagGATGTCTATTTGCGATTTCCATTGCTAAGGAGGAAGCCACCAAGTTAGGGACGGTCATCGGCATTGATCTTGGAACAACCTATTCATGTGTCGGTGTTTA

- - - - tatgtgc
- - - - - - - - aatgcag
- - - - - - - - - - - - - -taactgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaca