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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATAGTCAAGGAGTTGTTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacccatcaagggctgacatttactctaggt...

Basic information

species Glycine max
transcript GLYMA05G30330.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
CCATAGTCAAGGAGTTGTTGAGGTTAA-TGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaactt---ccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacccatcaagggctgacatttactctaggt-----
  |  |   || |   ||   |  ||  | | || ||||||||||| |||||||||||||| ||||||||||||    | ||||  || || || |||||||||    |   |  ||  | ||   | |   |  || |  | | | |  |   |  |  |  |||| |   |    |   ||  ||||  || || |     |     
-TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag

upper sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G57620.1 (Arabidopsis thaliana), 5'ss of exon 2
CCATAGTCAAGGAGTTGTTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatacgcat------aattttgaatctccctacactataggtagatagaact--taagtgttttacccatcaagggctgacatttactctag-gt--
  | ||||| ||       ||  |||   | ||| | || ||||||| |||||| ||||| || |||||||| ||  ||||||||||||| ||||| ||||| | ||  | | |  | |           |   | ||  | | ||||  ||       ||||     | ||| | | | |   ||   | | |  | | |  | | ||  
TAAAAGTCATGGTAACAAAGATTTTAGCATCAACATCGACTGGAAAACTGGAATCGCAGCTAAAGATTGGGACTCCATTGCTAGAAAAGAAAAGATCGAGgtcagctctccatatttccaagcctctgagacaattaaattacttacaagatcacatcttagagtaggttagtctctaaactgacactcgataatgtcttcaattgtgtag

upper sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 2
CCATAGTCAAGGAGTTGTTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacc-catcaagggc-tgacatttactctaggt-
||||| ||||||||  |  || || | ||| |||||||| |||||||  ||||||| ||| ||||||||||| || ||||| || || |||||||||||||| | ||    | |        |    || ||| |   ||   ||    ||  || ||  | | |||   |||  || | | |  |   ||  | |  |    
CCATAATCAAGGAGGCGGAGATGTAAGTGTCAACCTTGACTGGAAAACAGGAATTGGAGCAAAGGATTGGGAATCTGTTGCCAGGAAGGAGAAGATTGAGgtgacctcttcaaattattttttcccatttaatgt---tatggtacttataattaaaatgttaatgtccaaccatattaggtgtgttttatccaattgaatct

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|298169454|gb|HO020814.1|HO020814
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|9987066|gb|BE661174.1|BE661174
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|192325154|gb|FK019085.1|FK019085
EST:     GAATTGCAGCCAAGGATCGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298181707|gb|HO025882.1|HO025882
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298165642|gb|HO011691.1|HO011691
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|193698781|gb|FK637192.1|FK637192
EST:     AATTTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAAAAGGAGCAGTAGAGGCCATCCAT
genomic: AA-TTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298194557|gb|HO043029.1|HO043029
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|192314293|gb|FK007031.1|FK007031
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|193518314|gb|FK476627.1|FK476627
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|151407142|gb|EV276957.1|EV276957
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|207785148|gb|GD755665.1|GD755665
EST:     AGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: AGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298177574|gb|HO027241.1|HO027241
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|208106478|gb|GD906463.1|GD906463
EST:     GATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|209712647|gb|BW684577.1|BW684577
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTA
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTA
EST: gi|208263549|gb|GE063809.1|GE063809
EST:     CTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: CTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|151394892|gb|EV264763.1|EV264763
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|193700705|gb|FK635124.1|FK635124
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAAGCAGTAGAGGCCATCCA
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGA-GCAGTAGAGGCCATCCA
EST: gi|298173418|gb|HO016754.1|HO016754
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAG
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAG
EST: gi|192314294|gb|FK007032.1|FK007032
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|192322896|gb|FK014827.1|FK014827
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|151411095|gb|EV280906.1|EV280906
EST:     GAATTGCAGCCAAGGATCGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|151405471|gb|EV275285.1|EV275285
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298178629|gb|HO024364.1|HO024364
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTGGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCAT
EST: gi|298163990|gb|HO013635.1|HO013635
EST:     GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTCGAGCTTGAGCTG
genomic: GAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTCGAGCTTGAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATAGTCAAGGAGTTGTTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacccatcaagggctgacatttactctaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcccta