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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC

Basic information

species Glycine max
transcript GLYMA20G32230.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32230.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
-----------------------attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggc-tcttagtgaa--tgatggcataacatcaatt--tgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC
                       ||      | ||| ||| |||||     |||   | | | |  ||       ||   |   || || |  |||  |   |  |    |||  | |  |  | ||||| |||||||| ||||  || | ||| ||||||||||| |||||||| ||||| |||||||| |  |  | |||  |||| ||||| || |||||||| |
gtttgttttcaacattcagtctcatcttgcctttttcttt-tagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC

upper sequence: GLYMA20G32230.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC
           | |   ||  || | |     ||| ||  || || | || | || ||    |   ||  | | || | ||| |      |||||||||||| |||||||||||||| ||||| || ||||| ||||| ||||||||||| || |||||||||| ||||||||  || || |||||||||||||| || |
----------gtctgcaatctaactcc----ctcatgtctttctgca-atgtctcgaa---aaaagtcccactaaa-gttggaa------caatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC

upper sequence: GLYMA20G32230.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0019g04640.t01 (Vitis vinifera), 3'ss of exon 9
attccatttatttttttataga---agttcaagtatcaagttgttttgtatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC
   || |||||   |     |    |  |    |||  |  | |  |||  || ||   ||  || |     |    ||   ||    |     || ||||||   |||||||| ||||| |||||||| |||||||||||||||||| ||||||||||||||||||  | ||  ||| |||| || |||||||||||||| |
---ccctttatgagtaagaggttttaacttgtttatttatctatcctgttcatctagtgaaaaagtgtagactgagcaacactgatgaattgcaaaattgcagATCATGATGAAAGACCCATTTGGAAACTATGTTGTGCAAAAGGTTATTGAGACTTGTGATGATCAGACTCGAGAGTTGATTCTCTCTCGCATCAAGGTCC

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|193715066|gb|FK649769.1|FK649769
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
EST: gi|31473731|gb|CD415759.1|CD415759
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
EST: gi|208253410|gb|GE051132.1|GE051132
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
EST: gi|27426832|gb|CA938352.1|CA938352
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATT
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATT
EST: gi|208251830|gb|GE045549.1|GE045549
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
EST: gi|193622417|gb|FK568183.1|FK568183
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG
EST: gi|193382656|gb|FK345853.1|FK345853
EST:     TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAG                         GCTATGATGAAGGACCCTTTTGGAAACTATGTTGTGCAAAAGGTTCTTGAG
genomic: TTTTGGTGAATGAAATGCTTGGTACTTCTGATGAGAATGAACCCTTACAGgtatggctcc ... caatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC
                                    gcataac  putative branch site (score: 3)
     ttatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -ccattta
- - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc