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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttttgatgtcaaatagtgttgaagaagaaatgggggtatgatcatttggtttgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA

Basic information

species Glycine max
transcript GLYMA18G47200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G01310.1 (Arabidopsis thaliana), 3'ss of exon 1
-----aagttttgatgtcaaatagtgttgaagaagaaatgggggtatgatcatttggtttgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA
     || |  || |||      |||   |   | ||||| |  | |||  |||||     |     ||| ||| |    |  | ||   | || |   |  ||||| || ||  |  |||||||||| ||||| ||||||||||||||||| ||||| || |  ||||||||||| || || || |  ||| | || || ||||
tgataaaatcgtgctgttgggatgtgcc-atttacaaatgtgaatgtga--atttgtcaatctcatcattgttgtatatct--gcttggacatcttctctaccagGTTCCAAAGGTACAGAAGATTGTAGTGAATTGTGGTATTGGAGATGCGGCGCAGAACGACAAGGGTTTGGAGGCTGCGATGAAGGATATCGCGCTTATCA

upper sequence: GLYMA18G47200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01780.t01 (Vitis vinifera), 3'ss of exon 1
-aagttttgatgtcaaatagtgttgaaga--agaaatgggggtatgatcatttggtt-tgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA
    |  || ||     |  |||| |     || ||       || | || || ||     | |    |||| |||| |||  ||    ||   |     | |||| || || || || ||||||||  ||||||||||||||||||||||| | || |||||||||||||| || || || || |  || || || || ||  
ttcttcctggtgctcctttttgtttattttcagcaacattttcataagcacttagtagcttcctttccttttacaattttgcatt---gctgaatgtggat-agGTTCCAAAGATCGAAAAGATTGTTCTGAACTGTGGTATTGGAGATGCTTCACAGAATGCAAAGGGTTTAGAAGCAGCCATGAACGAGCTGGCTCTTATTG
















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|192324257|gb|FK018228.1|FK018228
EST:     AAATTATTCCCTCGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|151409347|gb|EV279155.1|EV279155
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|209710872|gb|BW653633.1|BW653633
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|213588516|gb|DB961633.1|DB961633
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|213601180|gb|DB964673.1|DB964673
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|254328287|gb|GR835252.1|GR835252
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|209713844|gb|BW684037.1|BW684037
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|31562001|gb|CD487839.1|CD487839
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|151393151|gb|EV263026.1|EV263026
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|151404935|gb|EV274749.1|EV274749
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|213610600|gb|DB960625.1|DB960625
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|192321826|gb|FK013218.1|FK013218
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|151404038|gb|EV273848.1|EV273848
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|18735233|gb|BM528646.1|BM528646
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCT
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
EST: gi|298166386|gb|HO010965.1|HO010965
EST:     AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAG                         GTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG
genomic: AAATTATTCCCTTGCTCATGGAAGAGTTCTCTTACACCAACAAACACCAGgttttaccaa ... ttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttggtttgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA
                                  ttttatcttccttcat  CT-rich tract
             ttcaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagttttgatgtcaaatagtgttgaagaagaaatgggggtatgatcatttggtttgccttcaatttttgcaatgttgggttttatcttccttcatttcagGTGCCTAAAATTGAGAAGATTGTGGTGAACTGTGGTATTGGAGATGCTGCGCAAAATGCAAAGGGTTTGGACGCGGCAATAAGTGATCTAGCACTGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - tgatgtc
- - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - gggggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggg