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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaactgaaattttatcaccttaccttcttgttcgttgattgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT

Basic information

species Glycine max
transcript GLYMA08G19640.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G15200.1 (Arabidopsis thaliana), 3'ss of exon 4
gtactaaactgaaattttatcaccttaccttcttgttcgttgattgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT
    ||||   || |  |  ||     |||| || |  |      |    | |  |||      |     |   | |||   ||  |   | || |     | |  | || |     | || | ||  |||||||| || ||||||||||||||||| |   ||||||||||||||| ||||||| | ||  | |   
---gtaaatcaaattcctcccataaatcctttttatgagaacgaagcgactgtttactcagtggtt--gttgttattttgctcttatcagCGTTACGAAGCTTTTGCATTGC-----CGGAGCCTGCACCAAGGGTTTTACCTAAGAATGAGGATCCTAAACTGGTTAATAGGAACAGAAGAATGCTAGGGAATC---

upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------gtactaaactgaaattttatcaccttacc-ttcttgttcgttgattgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT
                                                                 |    ||  ||||  |  |    |||    || | ||| || ||| |||  || |       ||  ||| | |    |||     || |   ||| ||| || ||| | |||    ||||| |||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||||||||||||||| || ||| 
gtaaaactggaagacttgccatcttatatatgtttatttattacatatttaatgcagattttggtttgggaatagaaacctagtttttttattgctcctattc-ttcattattgtctttagtactattacttaaattat-tattatttcattatgt-ttttagGATTTTGAAGCTCCAGTGACAGAGCATGTTCCAAGGGTTTTGCCAAAGAACGAGGACCCGAGCTTGGTTAATAGGAACAAAAGAATGTTGGGTCAACTTA
















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|193373413|gb|FK342411.1|FK342411
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|208034056|gb|GD831488.1|GD831488
EST:     AAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAA
genomic: AAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAA
EST: gi|208176632|gb|GD979105.1|GD979105
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|213601376|gb|DB968706.1|DB968706
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|208324334|gb|GE125691.1|GE125691
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|193413949|gb|FK376543.1|FK376543
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATC-AAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|6482510|gb|AW201767.1|AW201767
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTAT
EST: gi|208143447|gb|GD942465.1|GD942465
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|298169192|gb|HO020552.1|HO020552
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATTAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCC
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCC
EST: gi|207839868|gb|GD810061.1|GD810061
EST:     ATATCAGCAATC-AAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCATGTTCCAAGGGTATTGCCTAAGAAT
genomic: ATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAAT
EST: gi|208118695|gb|GD917902.1|GD917902
EST:     ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAG                         GCTTCTGACGTTCCTAATACTGATCAT
genomic: ACCAAAGTGGATGGTCTAAGAGAGATATCAGCAATCAAAAAACTTCAAAGgtactaaact ... tccatttcagGCTTCTGACGTTCCTAATACAGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT
                        aactaac  putative branch site (score: 1)
                                             tccatttc  putative PPT
                 tatatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaactgaaattttatcaccttaccttcttgttcgttgattgttggtttcaacttgtatatctaactaacactttagcctgttgtccatttcagGCTTCTGACGTTCCTAATACAGATCATGTTCCAAGGGTATTGCCTAAGAATGAGGATCCAAGTTTGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA