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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgctgagcatcagtattgcatttttagaacaaagcaaatgtcatatgcagttaactctaccacaagacgatgtgtgatttttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC

Basic information

species Glycine max
transcript GLYMA13G42360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
-----gatgctgagcatcagtattgcatttttagaacaaag------caaatgtcatatgcag-------ttaactctaccacaaga----cgatgtgtgatt--tttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
      ||||| |   | |||   | |  |||| |  ||            ||| || |   |       |||||| || |  | |          |||||||  ||   |  || || | ||||||| || | ||||||||| || ||||| || |||||||| || || ||||||||||| |||||||| |||||||| |||||||| |||||||| || ||
gtatctatgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
gatgctgagcatcagtattgcatttttagaa---caaagcaaatgtcatatgcagttaac--tctaccacaagacgatgtgtgatttttaattct--tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
  |  | |       |  |   | | ||| |     ||  |  | || | ||   || |     ||    |  ||  | | | ||   |  ||||  | ||  ||||||||||||| ||||||||| || ||||| || ||||| || || ||||| |||||||| ||||||||||| |||||||||||||| ||||| || |||||
-gtattta-tgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
gatgctgagcatcagtattgcatttttagaacaaagcaaatgtcatatgcagttaactctaccacaagacgatgtgtgatttttaattct--tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
        | ||  || | | |  || | ||   ||| | | |  | ||   |      ||    |  ||  | | | ||   |  ||||  | ||  ||||||||||||| ||||||||| || ||||| || ||||| || || ||||| |||||||| ||||||||||| |||||||||||||| ||||| || |||||
--------gtatgtgtgtaggaacttgaaaa---agcta-tcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------gatgctgagcatcagtattgcatttt---tagaacaaagcaaatgtcatatgcagttaactctaccacaagacgatgtgtgatttttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
                                               || |       ||| ||| |||||   | |       ||||  | |  | | |||| ||||   ||||    || | || ||||   || ||  || |||||||| |||| ||||||||| || ||||| || |||||| |||| |||||||||||||| |||||||| ||||| ||||| ||||||||||||||||| ||
gtaagtgaagtatttcctttgagaacacattctatacataccttcattgtttctgtctagttttgtattttcttttgtttgtttcaaagctta-gtactgtta-ctcttaaacaacctcatat-tggtttt--gttatttatcattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
---gatgctgagcatc-agtattgcatttttagaacaaagcaaatgtcatatgcagttaactctaccacaaga----cgatgtgtgatt--tttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
     ||  ||   |  |      ||   ||             ||  || | |  |||||| || |  | |          |||||||  ||   |  || || | ||||||| || | ||||||||| || ||||| || |||||||| || || ||||||||||| |||||||| |||||||| |||||||| |||||||| || ||
gtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggat-tcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 3'ss of exon 3
gatgctgagcatcagtat-tgcatttttagaacaaagcaaatgtcatatgcagtta-actctaccacaagacgatgtgtg---atttttaattcttg--ttcttt---agGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
           ||| ||     | || |  |  |  |    |||| | ||  |||     |||||        |  ||     |  | | |  || |  ||||||   ||||||||||| ||||||||| ||||| || || ||||||||||| ||||||||||| || |||||||| || ||||| || ||||||||||| || || ||
----------ttcaatacgcaaaattatgaactactgttgctgtcttttgttgttctggcctaccttctcctaacatgcacaaacctcttaccctgggtttctttcaaagGTTTTGAGAAGCCTTCTGCGATCCAACAAAGAGGAATTGTTCCATTCTGCAAGGGGCTCGATGTGATCCAACAGGCACAATCTGGAACTGGGAAAACTGC

upper sequence: GLYMA13G42360.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
gatgctgagcatcagtattgcatttttagaacaaagcaaatgtcatatgcag--ttaactctaccacaagacgatgtgtgatttttaattc--ttgttcttta--gGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
        ||||   |  ||  |  ||           | | || ||   ||    || |  ||| ||    | ||    | | | | |    |||  || ||  |||||||||| ||| ||||| ||||| ||| | ||||| ||||| |||  ||||||||| ||||| ||||| || || |||||||||||||| ||||||||
------ttgcatgttttgtgggtgcttgtggtgttcgtagtttcctaccgagaaccaattgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|5606855|gb|AI900953.1|AI900953
EST:     TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATG                         GTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
genomic: TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaa ... tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
EST: gi|192305404|gb|FG998272.1|FG998272
EST:     TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATG                         GTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
genomic: TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaa ... tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
EST: gi|12773183|gb|BG238110.1|BG238110
EST:     TTATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATG                         GTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
genomic: TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaa ... tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
EST: gi|254347906|gb|GR854155.1|GR854155
EST:     TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATG                         GTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
genomic: TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaa ... tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
EST: gi|209726515|gb|BW658082.1|BW658082
EST:     TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATG                         GTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA
genomic: TGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaa ... tgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcagttaactctaccacaagacgatgtgtgatttttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC
                                   ttttaat  putative branch site (score: 3)
                                         ttcttgttcttt  CT-rich tract
                                 atttttaattcttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgctgagcatcagtattgcatttttagaacaaagcaaatgtcatatgcagttaactctaccacaagacgatgtgtgatttttaattcttgttctttagGTTTTGAGAGGCCTTCTGCAATCCAGCAGAGGGGAATTGTTCCTTTCTGCAAGGGTCTGGATGTGATTCAGCAGGCTCAGTCTGGAACTGGAAAGACAGC

gatgctg
- - - - - - - - - tgcattt
- - - - - - - - - - - - - - - -caaagca
- - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtga