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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttctttttgccccttttttaaaatatgcatttaaactttctttctttggtggcttccttttcagccatgacggcatcttatgcctttctcgtt...

Basic information

species Glycine max
transcript GLYMA16G25200.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25200.2 (Glycine max), 5'ss of exon 3
lower sequence: AT4G36530.1 (Arabidopsis thaliana), 5'ss of exon 4
ATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttctttttgccccttttttaaaatatgcatttaaactttctttc--tttggtggcttccttttcagccatgacggcatcttatgcctttctcgtt-
|||| |||||| ||||| || || |||||||| || |||||||||||||| || | |||||||||||||||||||| || |||| || || ||||||| || | | | || | | | || | || |||| || || | ||| | | || || | || | |
TTTGGGAATGGAGAGGTCACAAGATTCATTATGTTGTTCAAGGAGAAGGCTCGCCTCTAGTTCTTATTCATGGTTTTGGTGCTTCTGTCTTTCATTGGAGgtaccttcaatctcacctccatgctctattgatcagtgtaggctttaagtcaactttttaccttatcatacgaattcgagctaatatcggtagatttttatag

upper sequence: GLYMA16G25200.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv04s0023g02010.t01 (Vitis vinifera), 5'ss of exon 3
ATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttctttttgcc-ccttttttaaaatatgcatt-taaactttctttctttggtggcttcctt--ttcagccatgacggcatcttatgcctttctcgtt
|||||||||| | ||||| |||||||||||||||| ||||||||||| | ||| ||||||||||||||||| ||||| || || ||||| || |||||||| | | || | || ||| | || || | | || | || ||| | || |||| | | || | | | ||| |
TTTGGACATGGCGAGGTCACAAAATACATTATGTAGAACAAGGAGAAGGATTTCCGATTGTTCTTATTCATGGATTTGGTGCTTCCGCATTTCATTGGAGgttgatcattttatacccatcttccctgtcatgagcttcatgaattagtagagttcattggagtagttcattcaatctttacagtgtataatgttatagg----
















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|213604690|gb|DB960469.1|DB960469
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|209728317|gb|BW658529.1|BW658529
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|209725699|gb|BW663190.1|BW663190
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|192301616|gb|FG998468.1|FG998468
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|18692833|gb|BM521681.1|BM521681
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|151399533|gb|EV269404.1|EV269404
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|213591367|gb|DB955715.1|DB955715
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|20448288|gb|BQ252412.1|BQ252412
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|13125828|gb|BG316398.1|BG316398
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|151405996|gb|EV275811.1|EV275811
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|120529684|gb|EH257818.1|EH257818
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|20814627|gb|BQ299105.1|BQ299105
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|151405769|gb|EV275583.1|EV275583
EST:     GCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: GCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
EST: gi|209716247|gb|BW657550.1|BW657550
EST:     TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAG                         GTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT
genomic: TCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttc ... atatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGTTCTTATTCATGGTTTTGGGGCCTCTGCATTCCACTGGAGgtttgttttctttttgccccttttttaaaatatgcatttaaactttctttctttggtggcttccttttcagccatgacggcatcttatgcctttctcgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggtgg