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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattcttaatctgctgcttcttattgtttaaactaatatttttgtaactgaaactactaagcttgttttatggtaaaacttgctaacaaaacaatttgttctgttcag

Basic information

species Glycine max
transcript GLYMA07G03930.2
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 18
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 19
CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatca-ttcttaatctgc-tgcttcttattgtttaaactaatatttttgtaactgaaactactaagcttgttttatggtaaaacttgctaacaaaacaatttgttctgttcag
| || | |||||| || || ||  ||||  |||| || ||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||  |  ||||||   |  ||  | |||   | | |         ||  |  |  |  | |         ||| |    || |||  |   |    |     |          
CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattcc--aggccagcttttacatttaacacaaacactctcggcctttgcttgcag----------

upper sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 18
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 16
CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaa---tcattcttaatctgctgcttcttattgtttaaactaatatttttgtaactgaaactactaagcttgttttatggtaaaacttgctaacaaaacaatttgttctgttcag
|||||| | || | || || ||        | ||  | |   |  | |   | || ||| |||| ||  | |||||||||||||||||||| ||||||||    | ||  | ||||  |   | |  | ||    |   |  ||  ||| | |  |    || | |  |    |   |      |||||| ||    |              
CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCACTTTTATGACTGTTACAATGAGCTGTGATCATCGTGTTATTGATGgtaagttccgtttctgatcttttaaatgtattagtgccgaacgaacttagtgtgagttcataacctcaac--gaacgaacttggtgtgtgctaataagctca--------------
















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|6952010|gb|AW424078.1|AW424078
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|192309363|gb|FK000571.1|FK000571
EST:     TGCTTCCTCCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|22927461|gb|BU544600.1|BU544600
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|298165294|gb|HO011343.1|HO011343
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTGTATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|213593954|gb|DB983162.1|DB983162
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATT                         AACCAATTGCAGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|9984928|gb|BE659036.1|BE659036
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC
EST: gi|192309362|gb|FK000570.1|FK000570
EST:     TGCTTCCTCCATGTCTGTGACC-TCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATGGTTAAA-GCATTCAAAG-CTATATT
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATT
EST: gi|8827585|gb|BE211315.1|BE211315
EST:     TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATG                         GTGCAATTGGTGCCGAATAGTTAAAAGCATTCAAAGGCTATATGGAGAATC
genomic: TGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattc ... ttctgttcagGTGCAATTGGTGCCGAATGGTTAAAAGCATTCAAAGGCTATATTGAAAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattcttaatctgctgcttcttattgtttaaactaatatttttgtaactgaaactactaagcttgttttatggtaaaacttgctaacaaaacaatttgttctgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG