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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG

Basic information

species Glycine max
transcript GLYMA05G32030.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G09900.3 (Arabidopsis thaliana), 3'ss of exon 9
gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
                                                       |      || ||  ||     || |  | | |    |||    |  | |  ||   ||   |||   | |||||||| || ||||| ||||| ||||| ||||| || || || ||||||||||| |||||||| ||||| || ||  ||
------------------------------------------------------gtctctcaatttgtctttaagcttgt-ttacataagttgattgatgctttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttat--acttctttttgtgaacattaatatggagcatttttgttaccttt--cagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
                                   |   | | | |  | |   ||       ||    ||   ||  ||  | |  |  |   ||   ||||  |     ||| ||   | |||   ||||||||||| ||||| ||||| |||||  |||| ||||| || |||||||||||||| ||||| ||||| |  |   ||
---------------------------------gtaaagactctttgagctctaatctatctttacctctttgattgcatcaattgttactgaagagtcttaactttacaaattcttcacatcttctgcagAATATTCTCGTTGTCTCAAAGTACTACTCAAGGATTACCTTTAAGAGACTTGCAGAACTTTTATGCCTAACCACTGAG

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
                                                ||  || |   |   | |  || |  || | ||| |   ||  |  |   |    |  ||   ||   |||   | |||||||| || ||||| ||||| ||||| ||||| || || || ||||||||||| |||||||| ||||| || ||  ||
------------------------------------------------gtaagtctctcaatttgtctttaagcttgtttacataagttgattgatgct---ttaaagttattaatttattctgcagAATATCCTCGTTGTCTCAAAGTACTACGCAAGGATAACCTTAAAGAGACTTGCCGAGCTTTTATGCCTGAGCATGGAG

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 9
gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
                 |  | |||||    ||   | | ||   |    |  | || | ||||    |||  |||||    |   ||  || |  |||  |||| |  | | |  |  | |||||||| || |||||||| |||||||||||  |||| || || || ||||||||||||||||| ||||| || ||  | |||
----------------gtagtgtttctctgtacat-ttagttccatacaataatttt-tttgatca--tttgagttttgagtt--attgggtaattatttgtatgcaaaactgtctt--cttttcagAACATCCTTGTTGTCTCAAAATACTACTCAAGGATAACGTTAAAGAGACTTGCAGAGCTGTTGTGTCTTAGCGTCCAG

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|13789644|gb|BG652235.1|BG652235
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAGCAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|19053473|gb|BM732140.1|BM732140
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|254341094|gb|GR854822.1|GR854822
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|18734862|gb|BM528428.1|BM528428
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|193487785|gb|FK452766.1|FK452766
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|22524861|gb|BU083672.1|BU083672
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAGCAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|9564218|gb|BE473727.1|BE473727
EST:     CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACAT                         AATATTCTTGT
genomic: CTTTGGGTGAAAAAGCAGCAGAAGATCTGAGGCAAAGAATAATTGAACATgtaaataact ... tacctttcagAATATTCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG
                       cattaat  putative branch site (score: 3)
                                      tttttgttacctttc  putative PPT
                     aacattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataactgatgccattatatttcttctcacccatcaattttgttggttggtattgtatgatatgctttatgttttatacttctttttgtgaacattaatatggagcatttttgttacctttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT