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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcagaaagaacttagcagcctcttgtcacagaagatagattttgttacaacaaagggttggtctccttgaatgatcaaggaaactaacgccttatattctaacactaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------gtatttcagaaagaacttagcagcctcttgtcacagaagatagatt--------ttgttacaacaaagggttggtc-tccttgaatgatcaaggaa------------actaacgccttatattctaac----actaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG
                           |  |  |||||||  | |  |   | ||   |       || |||        ||| || |  ||   | || || | | | ||||     || |               ||    || || |  |||    || || | ||||| |  |||   ||||||| ||||| ||||||||| ||||||||||||| ||| || | || |||||| |||||| ||||
gtatggttatgaggtgccataacttgttgctgaagaaagatttcataaatttttttatattattcttatattcttaagctttgataaattaatatgatgttccttcatcaatgtgtggggtacaactgattttagtcaatattttttactgaaacttttaccaattttgcagACTTTGATGAAGAAGGGTTATGAACTTGTTTCTAGTGGAACTGAGAACCATTTAGTCTTAGTGAATTTGAAGAACAAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtatttcagaaagaacttagcagcctcttgtcacagaagatagatt--------ttgttacaacaaagggttggtc-tccttgaatgatcaaggaa------------actaacgccttatattctaac----actaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG
                           |  |  |||||||  | |  |   | ||   |       || |||        ||| || |  ||   | || || | | | ||||     || |               ||    || || |  |||    |  || | ||||| |  |||   ||||||| ||||| ||||||||||||||||||||||| ||| || | || |||||| |||||| ||||
gtatggttatgaggtgccataacttgttgctgaagaaagatttcataaatttttttatattattattatattcttaagctttgataaattaatatgatgttccttcatcaatgtgtggggtacaactgattttagtcaatattttttactgaaacttttatcaattttgcagACTTTGATGAAGAAGGGTTATGAACTTGTTTCTGGTGGAACTGAGAACCATTTAGTCTTAGTGAATTTGAAGAACAAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------gtatttcagaaagaacttagcagcctcttgtcacagaagatagatt--------ttgttacaacaaagggttggtc-tccttgaatgatcaaggaa----------actaacgccttatattctaac----actaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG
                           |  |  |||||||  | |  |   | ||   |       || |||        ||| || |  ||   | || || | | | ||||     || |             ||    || || |  |||    || || | ||||| |  |||   ||||||| ||||| ||||||||||||||||||||||| ||| || | || |||||| |||||| ||||
gtatggttatgaggtggcagaacttgttgctgaagaaagatttcataaatttttttatattattcttatattcttaagctttgataaattaatatgatgttccttcatcaatgtgtggggtacaattgattagtcaatattttttactgaaacttttaccaattttgcagACTTTGATCAAGAAGGGTTATGAACTTGTTTCTGGTGGAACTGAGAACCATTTAGTCTTAGTGAATTTGAAGAACAAG

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|208213023|gb|GE009184.1|GE009184
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208181657|gb|GD978508.1|GD978508
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|207838361|gb|GD811115.1|GD811115
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|193351009|gb|FK315773.1|FK315773
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|207828088|gb|GD797979.1|GD797979
EST:     TCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: TCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|207781497|gb|GD754020.1|GD754020
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208197654|gb|GD998875.1|GD998875
EST:     TTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: TTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208201733|gb|GE000507.1|GE000507
EST:     TCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: TCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208024218|gb|GD824240.1|GD824240
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208337743|gb|GE135181.1|GE135181
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208242536|gb|GE037894.1|GE037894
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAAGAATCA
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGA-GAATCA
EST: gi|208307263|gb|GE101985.1|GE101985
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208324639|gb|GE120634.1|GE120634
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208135490|gb|GD934515.1|GD934515
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAG
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAG
EST: gi|207731953|gb|GD705634.1|GD705634
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208290230|gb|GE084492.1|GE084492
EST:     TTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: TTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|22931030|gb|BU548169.1|BU548169
EST:     ATAGAGCATACCAAGAGCAGNNNCTCNGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|16346437|gb|BI972032.1|BI972032
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208322012|gb|GE125973.1|GE125973
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|207775539|gb|GD746886.1|GD746886
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGA
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGA
EST: gi|193562546|gb|FK519077.1|FK519077
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGACTTAAGTTTCTGGTGGAACT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAG-CTT--GTTTCTGGTGGAACT
EST: gi|207705137|gb|GD687730.1|GD687730
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGGAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAAATCA
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAA-TCA
EST: gi|208235434|gb|GE029676.1|GE029676
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGATTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|16348582|gb|BI974177.1|BI974177
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208218304|gb|GE020032.1|GE020032
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
EST: gi|208044112|gb|GD842426.1|GD842426
EST:     ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAG                         GCACTGAGTGAGGAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT
genomic: ATAGAGCATACCAAGAGCAGGTTCTCCGTAATTGCTCAAAATTTGCACAGgtatttcaga ... aaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccttgaatgatcaaggaaactaacgccttatattctaacactaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG
                              ttatattctaacacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcagaaagaacttagcagcctcttgtcacagaagatagattttgttacaacaaagggttggtctccttgaatgatcaaggaaactaacgccttatattctaacactaaatatgcagGCACTGAGTGAGAAGGGCTATGAGCTTGTTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG