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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactgatgctttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT

Basic information

species Glycine max
transcript GLYMA02G44690.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactga-tgct----ttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
                                              |  |||  | ||||     | | ||   ||   ||| | ||||      ||| |  |||  | | |     |    || ||  |||| ||||||||| || || ||||| ||||| ||  |||||||||| |||||   ||||||||||||||||||||||||||| |||||  |   ||||||||  ||| ||
----------------------------------------------gtatattgaagaaattcactagctatc-attttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT

upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactg--tttggtaaagatgccaaaaaccaaaagtataactgtataactgatgctttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
                     ||  | ||  ||||||    ||| |   ||     ||||| |   |||    ||   ||    |    |||||     | | |   ||    ||    |  ||  ||   | ||||||||| ||| ||||| ||||||||| ||||||||||||| ||  | || || |||||||||||||||||  | |||||||| || ||||  ||||| || 
---------------------gtatatatgctctttcgaagcttctttttaatgttgaaaatttgctttttccaatgagcttttacttgaaagt-----tatgtgtttg-catttgaaatgactttaagtttgtcagTGCTAGAATTTTCAACATATATCCACGGAAAGGAGCTATCCTTGCTGGCTCGGATGCAGATATTATCATATTGAATCCAAACTCAAGCTACGAGATTAGC

upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 11
gtatattttcagt-taatcaaa-gtgaaaattatctttcagttcttatgactataaaggaaaac-tgtttggtaaagatgccaaaaaccaaaagtataactgtataactga-tgctttttgtttctaca--atcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
||||  |||||   | ||||    || | |   ||  | |   || |  | | || | || |   |||||   ||      |  |    |    |  |||  |||     | ||  |||   || ||||  ||  ||||||||||| ||||||||| || ||||||||||||||||| || ||  | |||||||||||||| || |||||  | || |||||||| |||||  | || | |
gtatgctttcaaagtgatcatttatgtagaggttccctaaa--ctgaaaaatgtataagatagtgtgttttacaatttaatctcagtttacctatcaaaccatatggaaaagtgagtttaacttttacattattttttcagTGCTAGAATCTTCAACATGTATCCAAGGAAAGGAGCAATACTTGCTGGATCTGATGCAGACATAATCATATTAAACCCAAATTCAAGCTTCCAAATAACT

upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S101_168V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactgatgctttttgt---ttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
                                       || |    |  |||          |||    ||   | |   ||   |  |    |  |   ||     |||||| |||   || | ||| | | | ||||| ||||| |||||||| |||||  ||||||||||  | || ||||| ||||||||||| ||||||||  | || |||||| | |    |   ||    
-------------------------------------tattttgtccagaataggcattgtgagttacacaatccttcgtgaattaaggaacggaggtccttattctgtgctttgtgtggattgtgcaa-cttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC

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|120496721|gb|EH224888.1|EH224888
EST:     GTCACTGACTATGTCCGGATAACAAGCACTGAATG                         TGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
genomic: GTCACTGACTATGTCCGGATAACAAGCACTGAATGgtatattttc ... atcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
EST: gi|23730285|gb|BU763240.1|BU763240
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATG                         TGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATGgtatattttc ... atcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
EST: gi|22929708|gb|BU546847.1|BU546847
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATG                         TGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATGgtatattttc ... atcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
EST: gi|21994166|gb|BQ785694.1|BQ785694
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATG                         TGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGATAACAAGCACTGAATGgtatattttc ... atcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaccaaaagtataactgtataactgatgctttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
                      aactgat  putative branch site (score: 3)
                                              tcatttc  putative PPT
      aaaagtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactgatgctttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG