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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaagttgcttaatttggtatttcatgatctgggtggtagacttttcacgttcctataaaatttccatttctattataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC

Basic information

species Glycine max
transcript GLYMA08G27740.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 9
----tcaaagttgcttaatttggtatttcatgatctgggtggtagacttttcacgttcctataaaatttccatttctattataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
      ||||||      | | ||  ||  |  | |   |      |||| |    | | |    | | |||||| |  | |    | ||    ||   ||||||||||||| |||||||| || || ||||| |||||||| || ||||| || || ||||| |||| |||  | || ||||| || ||||| ||||||||||
gcaaataaagtttacggttctagttctttttc-tattcttcactacctttccttacttcaagcttaataccattttt--tgtttgtttgtg-tttcgaatgcagCTTGATGAATGGTGGGAACAACCTGCATCAACAGTTGTGGATTGGGTCACTGTAGATGGTCAAAGTGTTGCAGCTTGGCAAAACCATGTCAAACAGCTTC

upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 9
-tcaaagttgc-tta--atttggtatttcatgatctgggtggtagacttttcacgttcctataaaatttcca--tttctattataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
   | | || | |||  |||  | ||     | |||   |     | ||      || | ||    |||  |   || |||| |    ||  |   | | |||||||||||||||||||||||||| |||||||| || |||||||||||||| ||||| ||||||||||||||  |||| ||||||||||| ||||| ||||| |
actagacttacattagcattatggatacgtagttctatttaagttatttggtttatttccatttggttttaaaccttttatttt----tgaca--ttatactgcagCTTGATGAGTGGTGGGAGCAACCAGCATCAACCGTTGTTGACTGGGTTACAGTTGATGGGCAAAATGTTGCTGCTTGGCATAATCACGTGAAGCAGCTGC

upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S58_171V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------tcaaagttgcttaatttggtatttcatgatctgggtggtagacttttca-----cgttcctataaaatttccatttctatt-ataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
                                    |  | |  | ||  |||||   |  ||    |  ||| || ||    ||     | || | || |  ||   | |   |||       ||||    |    ||||| |||||||||||||||| ||||||||| | || || |||||||||||  | || ||||| || || ||   ||| |||      | ||||||||| ||||
gtaagtgtatgaaatttcctacgttacagttgagaattgaggacgttttttttggggatatattggttctgtgatacacaccccaaaagtcatttccattattttctgagtcgcattcgcttcgtggtgttatgca-tgcagGTTGATGAGTGGTGGGAACAGCCAGCAGCTACTGTGGTTGACTGGGTCTCTGTTGATGGCCAGAACGTTGGTGCTTGGTTGGCCCTTGTGAAACAACTTC

upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 9
----------------------------tcaaagttgcttaatttggtattt-cat--gatctgggtggtagacttttcacgttcctataaaatttccatt-tctattataaaatggtaacctcttctg-cagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
                            |   | |||    |||  |||    |||  || || |   | ||  |||     ||  | |    |    |   | | | ||| |  | |      | ||| ||| | || ||||||||||||||||||||||| || | |||||| ||| |   ||||||||| ||||||||  |||| |||| |  |||||||||||| || |
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC

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|208156163|gb|GD952371.1|GD952371
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|51334977|gb|CO978843.1|CO978843
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|27424390|gb|CA935910.1|CA935910
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|193554664|gb|FK513863.1|FK513863
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|193607435|gb|FK559162.1|FK559162
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAG
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAG
EST: gi|208092692|gb|GD887601.1|GD887601
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
EST: gi|207821669|gb|GD793926.1|GD793926
EST:     TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTG                         CTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA
genomic: TTTTGAGTGCTCAGCAGAGCTTGGAAGATTGCAAATATGTCAGGGGTTTGgtgagttacc ... tcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacgttcctataaaatttccatttctattataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
                                     tggtaac  putative branch site (score: 2)
                                           cctcttctgc  CT-rich tract
          tataaaatttccattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaagttgcttaatttggtatttcatgatctgggtggtagacttttcacgttcctataaaatttccatttctattataaaatggtaacctcttctgcagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -gttgctt
- - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - gggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttc