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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctggtaacagcactgccaaacgtgaatgtgttgtgggcactctgcgttctgtcattaaaaatcctataatactgtttttttttttttttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCCTACTTTTAATAAATGTAA

Basic information

species Glycine max
transcript GLYMA02G40310.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 9
tatc-tggtaacagcactgccaaacgtgaatgtgttgtgggcactctgcgttctgtcattaaaaatcctataatactgtttttttttttttttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCCTACTTTTAATAAATGTAA-
  || ||||     || |   |    | ||    |  |  ||  | | |  | | | |   ||       || |  |   ||| | | |   ||| | ||||| || || ||  ||||||||||||||||||||||||||||||| ||||||||||| ||  |||| || || ||||  |     |  ||| |   |  |  
-gtcatggttgggccatttttagggcttaagagatcatatgctgttttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTA-TCCTTTCACC
















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|209719242|gb|BW679797.1|BW679797
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|12691100|gb|BG157436.1|BG157436
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCTAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCG
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATC-AGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCG
EST: gi|207760750|gb|GD734073.1|GD734073
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|192332834|gb|FK026835.1|FK026835
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTCCTTTTTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|21479883|gb|BQ576566.1|BQ576566
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|209728549|gb|BW663549.1|BW663549
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|192323866|gb|FK018617.1|FK018617
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|193480230|gb|FK446748.1|FK446748
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|209725552|gb|BW677854.1|BW677854
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|254337821|gb|GR849560.1|GR849560
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|213611450|gb|DB976885.1|DB976885
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|58022083|gb|CX708824.1|CX708824
EST:     ATACTATACTTACAAAGGATAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|214007895|gb|DB986470.1|DB986470
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATAAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|193705903|gb|FK647109.1|FK647109
EST:     AAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: AAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|193364374|gb|FK328879.1|FK328879
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|58020605|gb|CX707347.1|CX707347
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|254337820|gb|GR849559.1|GR849559
EST:     ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttt ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgttctgtcattaaaaatcctataatactgtttttttttttttttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCCTACTTTTAATAAATGTAA
                           tactgttttttttttt  CT-rich tract
         tcattaaaaatcctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctggtaacagcactgccaaacgtgaatgtgttgtgggcactctgcgttctgtcattaaaaatcctataatactgtttttttttttttttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCCTACTTTTAATAAATGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - -cactgcc
- - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - -ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaaa