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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgatgagtttgtgcttttacttatctttcagttttttgtttgttgaaagagatgatgtactgtatgtttgtaataatcatgttaatgacatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTAAGAGAAGAGACAGGAGTTAATTCTGCAGAAGTGATTGCTGAG

Basic information

species Glycine max
transcript GLYMA20G33600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 2
tctgatgagtttgtgcttttacttatctttcagttttttgtttgttgaaagag-atgatg-tactgtatgtttgtaataatcatgttaatgacatcttt---tagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTAAGAGAAGAGACAGGAGTTAATTCTGCAGAAGTGATTGCTGAG
  || ||    |    | |||   | | |    | ||    |||||||||||  ||| |  |  |||||   | | | ||  || |||||   ||  ||    |||||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||  |||||||||||||||  ||| ||||| ||  |||| |||
--tgctgttcatcaaatcttatacaacat--gatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtat-ttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG
















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|14126670|gb|BG791108.1|BG791108
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
EST: gi|151410062|gb|EV279870.1|EV279870
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
EST: gi|151408157|gb|EV277965.1|EV277965
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
EST: gi|298164126|gb|HO013771.1|HO013771
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
EST: gi|151411978|gb|EV281789.1|EV281789
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATTCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagagatgatgtactgtatgtttgtaataatcatgttaatgacatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTAAGAGAAGAGACAGGAGTTAATTCTGCAGAAGTGATTGCTGAG
                                    tgttaat  putative branch site (score: 3)
                                             catctttt  putative PPT
                           taataatcatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgatgagtttgtgcttttacttatctttcagttttttgtttgttgaaagagatgatgtactgtatgtttgtaataatcatgttaatgacatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTAAGAGAAGAGACAGGAGTTAATTCTGCAGAAGTGATTGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
tctgatg
- - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtt