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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcaaaatagtcataaatttttgcttccatttccatcaaatgaatagtcaaagctacatatatatactaatatatatacatattgttccttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCCTGATTTCAAATCAACATTTCCCAAATGGCCATCCAAG

Basic information

species Glycine max
transcript GLYMA09G03470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 6
aggcaaaatagtcataaatttttgcttccatttccatcaaatgaatagtcaaagctacat--atatatactaatatatatacatat-tgttccttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCCTGATTTCAAATCAACATTTCCCAAATGGCCATCCAAG
|        |||  | |   ||||     ||| |    |  ||  |  ||| |    |||  | || ||  | |   ||| ||  | ||||  || ||| |||  | ||||| || |||||||| || |||||||| ||||| ||||| ||||||||||| || ||  | ||||| || |||||  | |||
aattttggaagtt-tgagaatttggaattattgcacatatttggtt--tcagactcgcatgaagatctatgatttcctattcacctatgttttttctattaagGGTATTGGGCACACCAAATGAGGATACATGGCCAGGAGTGACTTCTTTGCCTGATTTTAAGTCTGCCTTTCCTAAGTGGCCTCCTAAG
















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|120532704|gb|EH260837.1|EH260837
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGNCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|192309059|gb|FK001835.1|FK001835
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|192312501|gb|FK004987.1|FK004987
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAA-TATTCAG                         AATCTTGGGTACCC-AAATGAAGACACATGGCCTG-AGTA-CTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|151396909|gb|EV266782.1|EV266782
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACAT
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACAT
EST: gi|193425000|gb|FK392123.1|FK392123
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|208055121|gb|GD851136.1|GD851136
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACGCATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|192295604|gb|FG988178.1|FG988178
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|9563850|gb|BE473359.1|BE473359
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|193499843|gb|FK464760.1|FK464760
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|192330929|gb|FK023102.1|FK023102
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|192312081|gb|FK003858.1|FK003858
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|151394972|gb|EV264843.1|EV264843
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|151409597|gb|EV279405.1|EV279405
EST:     CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|193356410|gb|FK323123.1|FK323123
EST:     CTATTCCCTGGGGACTCTGAAGAATTAGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CTATTCCCTGGGGACTCTG-AG-ATT-GATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC
EST: gi|193328289|gb|FK294310.1|FK294310
EST:     CCTCTACTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTG
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTG
EST: gi|192300023|gb|FG991841.1|FG991841
EST:     CCTCTATTCCCTGGGGACTCTGAGACTGATGAATTATTTAAAATATTCAG                         AATCTTGGGTACCCCAA-TGAAGACACATGGCCTGGAGTAACTTCATTGCC
genomic: CCTCTATTCCCTGGGGACTCTGAGATTGATGAATTATTTAAAATATTCAGgtgaatatct ... ttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcaaagctacatatatatactaatatatatacatattgttccttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCCTGATTTCAAATCAACATTTCCCAAATGGCCATCCAAG
                    tactaat  putative branch site (score: 1)
                                      ttgttcctt  putative PPT
             atatatatactaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcaaaatagtcataaatttttgcttccatttccatcaaatgaatagtcaaagctacatatatatactaatatatatacatattgttccttatatgaagAATCTTGGGTACCCCAAATGAAGACACATGGCCTGGAGTAACTTCATTGCCTGATTTCAAATCAACATTTCCCAAATGGCCATCCAAG

- - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - -ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - agctaca