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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggcatttctgtataataaattggctgatatttagcatcctgtttacttgatgacatgattggcattttttgagattatgtgtgtaccatttaatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA

Basic information

species Glycine max
transcript GLYMA20G32200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttggcatttctgtataataaattggctgatatttagcatcctgtttacttgatgacatgattggcattttttgagattatgtgtgtaccatttaatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA
                                                           |  || |||| |||   |  | |    | | |    | |    | ||     |   | |  ||||    || || ||  |  |||     ||||||||||||||||||| |||||||||||||||| | |||| | ||||  ||||| |||||||| || ||||| || |||||||| ||||| ||||||||| 
---------------------------------------------------------gtatgtgtttggaattacctttggtgcattttttggtttctgtggtgatgatcttacactcaaattttgagttttaattgatagctttgca-acagATAAACCCTGAGAAGGCTAGGGAAGAGTTTCGTAGTGCCTCGCAGATGAATGGAGGAACTGGGGTGAAAGATTTTATGGATGGTATGGGACTTGGAATGC

upper sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
----gtaagttggcatttctgtataa----------taaattggctgata--tttagcatcctgtttacttgatgacatgattggcattttttgagattatgtgtgtaccatttaatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA
    |||      | || |||||| |          |   |||  |||||  |||   |||      |    |||| | |||||| |||   ||  | |   |  ||   ||||  ||| |  | |   | | || |||      | || ||  | | ||    |||||||||||||||| ||| || ||||||| || || |||||    ||||||||||| |||||||| |||||||| ||||||||||||||||| ||||||||| 
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtatta--tggcaatgcatccgttaaattttctatgaggctttgttgc-ctcattactcagtttaattggt-agttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
















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|17400268|gb|BM177050.1|BM177050
EST:     TGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTTTGAA                         -TAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAA
genomic: TGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTT-GAAgtaagttggc ... tcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAA
EST: gi|193485580|gb|FK448757.1|FK448757
EST:     GTGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTTGAA                         ATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAAT
genomic: GTGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAAT
EST: gi|7692844|gb|AW760943.1|AW760943
EST:     GTGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTTGAA                         ATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAAT
genomic: GTGCATTGGTGCCAGTAGAAGGACCTGATTATCCTCTTTTTGCTCTTGAAgtaagttggc ... tcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA
                                     tccttac  putative branch site (score: 2)
                                    ttccttacttcattt  CT-rich tract
                    ttatttaagtttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggcatttctgtataataaattggctgatatttagcatcctgtttacttgatgacatgattggcattttttgagattatgtgtgtaccatttaatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA