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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agccaccgtgattttgcctggtgaggaaaataacctgagaaacaatgtttctatcatatagtgactgaaaaaactgttgtattgatgattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCTTATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCAT

Basic information

species Glycine max
transcript GLYMA03G33000.7
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 1
---agccaccgtgattttgcctggtgaggaaaataacctgagaaacaatgtttctatcatatagtgactgaaaaaactgttgtattgatgattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCTTATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCAT-------------
     |  |    ||||    || | |   |      |||   ||   | | |     || |||||  ||    |||||    |    ||  | | | ||  | |||||    ||| |||||| |  |||||||||||||  | ||  | |||| ||||      |||||||||||| ||||||||||| |||||| ||||||             
tatgtcttctactatttcatttgataatagag-----ctggtgaatgct-tctaagaaatctagtgtttgttttaactg----aaaactgcatgtgaatttggcttgcagTAATGGCTCCACCTATTGAGACTCCAAACAAAGCTCTTAACTCTCATCA------ACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAG
















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|27446381|gb|CA953504.1|CA953504
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193489536|gb|FK456295.1|FK456295
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|7925031|gb|AW831057.1|AW831057
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|207800405|gb|GD775410.1|GD775410
EST:     AAGGGCCACAGATGGTTGAAACCGATTTGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193561881|gb|FK516858.1|FK516858
EST:     AAGGGCCACAGATGGTTG-AACCGNTATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193709781|gb|FK646049.1|FK646049
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193722890|gb|FK657466.1|FK657466
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|208022972|gb|GD820982.1|GD820982
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193656797|gb|FK606713.1|FK606713
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193677865|gb|FK614979.1|FK614979
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|24136670|gb|BU927180.1|BU927180
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193683993|gb|FK621451.1|FK621451
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|5510301|gb|AI856743.1|AI856743
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193558208|gb|FK513333.1|FK513333
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193583266|gb|FK538844.1|FK538844
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|9986811|gb|BE660919.1|BE660919
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193706053|gb|FK648477.1|FK648477
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|193563220|gb|FK520339.1|FK520339
EST:     -AGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
EST: gi|298199436|gb|HO042799.1|HO042799
EST:     AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACT                         GTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT
genomic: AAGGGCCACAGATGGTTGAAACCGATATGGATGCCGAAACTgtaagaaata ... ataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctatcatatagtgactgaaaaaactgttgtattgatgattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCTTATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCAT
                                  tattgat  putative branch site (score: 3)
                               ttgtattgatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agccaccgtgattttgcctggtgaggaaaataacctgagaaacaatgtttctatcatatagtgactgaaaaaactgttgtattgatgattataatttcagGTTGCAAATGTGGTTCCACCAAAGGAGACTCCAAACAGTGTTCCCATCTCTTATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT