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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattttttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga...

Basic information

species Glycine max
transcript GLYMA15G18170.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 4
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaatta-caaaatgagattttttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga
||||||||||||| | ||||| || ||||||||  ||||||||||||| ||||| |||||    | |||  ||  |      | |||  |   |      |  | ||      || ||| | |    |||  ||||||   |   | |    |      
TATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAGgttg--gtttatgaaccagttttcttagaaatgcgtgaactcttgcgtac---gctggtgt-attaactttgtgcttaattgtt-tgattctacag-----

upper sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattt---tttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga
||||||||||||| |||| || || ||||||||  ||||||||||||||||||| |||||    | || | ||||||    |     ||   || | |  | |   || |  || ||  |  | |    || || ||  |||                   
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgg--gtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactg--gacatttaatttaatttt--tcag------------------

upper sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 5'ss of exon 4
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattttttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga
|||||||||||| || || || |||| ||||||| |||| ||| ||||||| |||||||||||    |    || | ||  |   | | | ||      | |  ||   ||     ||  |||  | | |   | ||  ||   ||            
TATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAGgtaacaatcttatgatgagaactttgtaatatgttaaccaatga--tacaaaaggatcgtatctgacacttaaaatcatttattgcag------------

upper sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 4
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattttttttgttggtcacttattgaattgctg-tta----ctggtattgatcttaatcaatgctagtaagtaacttga-----------------------------------------------------------------------
|||||||||||| || || ||||| | ||||||||||||||| ||||||||||||||||||  |  | |||  ||   |  |         | | || | |    ||   |||  || |||     || |||   |   ||  |||    |  |||  | ||                                                                        
TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAGgtaggt-ttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcag

upper sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 5'ss of exon 4
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattttttttgtt-----ggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga
 |||||||| ||| | || || || ||||||||| |||||||||| || |||||||||||||    | | |  ||      ||   | ||||| |||     | ||  || || |||   | | |||||     |    | |   ||||  |   |       
GATCAATGCTATGCACCCGAAGACCAGGAAGATTTTGCAGCTTCTACGATTGAGACAGgtaaagattgatacttttttttgtgttttctttttggtttttttgctcttttctttaataattataactggacaaaaaaaaagtttctgctgatggtttt-----

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|151410194|gb|EV280009.1|EV280009
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|22932168|gb|BU549307.1|BU549307
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGNNNGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|192327716|gb|FK021351.1|FK021351
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|17023603|gb|BM094637.1|BM094637
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|192295535|gb|FG988109.1|FG988109
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|31456852|gb|CD398880.1|CD398880
EST:     GCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: GCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|8282865|gb|BE020426.1|BE020426
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|10232891|gb|BE801779.1|BE801779
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|58021409|gb|CX708150.1|CX708150
EST:     CCATGGATCCCAAACCAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|151400307|gb|EV270121.1|EV270121
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|31306158|gb|CD391361.1|CD391361
EST:     CCATGGATCCCCAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|58015969|gb|CX702711.1|CX702711
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|298195246|gb|HO043774.1|HO043774
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCCTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|20815022|gb|BQ299500.1|BQ299500
EST:     GGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: GGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|33388304|gb|CA851511.1|CA851511
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|209728367|gb|BW660005.1|BW660005
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|15663868|gb|BI701239.1|BI701239
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|192294770|gb|FG986619.1|FG986619
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|9820878|gb|BE556388.1|BE556388
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|151404968|gb|EV274782.1|EV274782
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|12689954|gb|BG156290.1|BG156290
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|151395296|gb|EV265167.1|EV265167
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|192307998|gb|FG998981.1|FG998981
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|58024451|gb|CX711192.1|CX711192
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|16996376|gb|BM085748.1|BM085748
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|8284546|gb|BE022114.1|BE022114
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|57574809|gb|CX547784.1|CX547784
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
EST: gi|192307999|gb|FG998982.1|FG998982
EST:     CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC
genomic: CCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgctt ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattttttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga

- - - -  CATGGA
- - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - GCAGCT