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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA

Basic information

species Glycine max
transcript GLYMA20G28970.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 6
-----gtaagt-tgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTG-TTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
     || | |   ||   |    |       |  |  ||  ||  |    |    |  ||    |  || || | |     |  |    ||||| |    |||||| | |||||||  |    | ||||||||| || || ||||||||| | || |||||||||||||| |||||  || |||| ||||| |||||||| 
tagcagtgaatacattcgacaaataaaatatgtgatggtgaaaggttgttgaacattgatg--cctaaatcagttgatcgttttttttcctgtttttcacagTTTCCCGATTGATGAACAAATGAATATGAAATCTGTCGTGGAATACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCCTGCCTTCAG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 7
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 5
-gtaagttgtttctctttcaggtctcttc--ctactggcagtcttagaaggtatagtgattttccattagctca--ctaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
  |||||    |          |   |||  | | |   ||| |  || | |  || | | ||  || | || |  || | |  |      |||    || || ||  |||||||  |    | ||||||||| || || || |||||| | || |||||||||||||| |||||  || |||| |||||||||||||| 
tctaagtcaccttagcagtgaatacattcgacaattaaaagtatatgatgatcaagggttgttaaatcaccttagcctgatttttatctaattttcacagTTTCCCAATTGATGAACAAATGAATATGAAATCTGTCGTGGAGTACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCTTGCCTTCAG

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
              |      | ||||  ||||  |  |||| ||      ||   | || ||||     | ||| |  || | | | |  |||||||||| || ||||||||||  |||||||| |||||  |||| || ||||||||||||||||| ||||| || ||  | || ||  | || || || |||
-------------gtgagtattttctttttacttac--tctttgattactaaggcttgtttcattga--gattaatttctggtttatattcttagGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA

upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 6
---------gtaagttgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatg-tgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
           || ||| |    |  |   ||| || || |||| | | || |      |  | | |       || |  |||| || | ||| |  || || || |||||||||||||| || ||||| ||||| ||||| || |||||||||||||| |||||||| || || |||||| || | ||||||||||||||||||
agttaaagcaaaaattgctctattaactcttctttttcttctggaattttttgc-----ttataaatgcatgcaagttttctaattattcatggttcttgttcagTTTTCCTGTTGATGATAATTCAACCATGAAGTCAGTTGTGGAATACTTCCAAGAAATGTATGGCTTTACAATTCAACATGCACACCTTCCTTGCCTTCAA

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|207836562|gb|GD805775.1|GD805775
EST:     AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGT                         GTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCA
genomic: AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGTgtaagttgtt ... gtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCA
EST: gi|207841573|gb|GD809355.1|GD809355
EST:     AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGT                         GTTTCCTGTTGAATGAGAACTCAACTA
genomic: AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGTgtaagttgtt ... gtttctttagGTTTCCTGTTGA-TGAGAACTCAACTA
EST: gi|24136288|gb|BU926798.1|BU926798
EST:     AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGT                         GTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCA
genomic: AGAAAGTATCGTGTTTCTGGGTTGACTTCTCAACCTACCAGAGAACTTGTgtaagttgtt ... gtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
                             cactaaa  putative branch site (score: 2)
                                            tgtttcttt  putative PPT
                                taaataatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtttctctttcaggtctcttcctactggcagtcttagaaggtatagtgattttccattagctcactaaataatgatgtgtttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG