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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctcatttatcatgtatttattagagctgcttcttcatttagtattttattctgatctaatgcccttataacttggtgccaacggaatttttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCAGGGTATCTTCATGCCTGTTTGAACACAGGGAAGCTTGCCTCCTTGGCAA

Basic information

species Glycine max
transcript GLYMA11G04420.1
intron # 1
splice site 3'
intron type U2

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|151408863|gb|EV278671.1|EV278671
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|12773182|gb|BG238109.1|BG238109
EST:     AAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: AAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|298183465|gb|HO028678.1|HO028678
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|192298731|gb|FG990997.1|FG990997
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|208158913|gb|GD954746.1|GD954746
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|192312780|gb|FK003992.1|FK003992
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|298197449|gb|HO044928.1|HO044928
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|192295310|gb|FG985964.1|FG985964
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|192312779|gb|FK003991.1|FK003991
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|192332695|gb|FK025352.1|FK025352
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|298196857|gb|HO041600.1|HO041600
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|298180781|gb|HO022220.1|HO022220
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAGACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|208169089|gb|GD969556.1|GD969556
EST:     GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: GAGCGAAAACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
EST: gi|10848287|gb|BF071708.1|BF071708
EST:     AACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAG                         TTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA
genomic: AACGTTATTGGGGCAGAAATAAAAAACCATAGAATAGATAGAGgtacgtacga ... tttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattctgatctaatgcccttataacttggtgccaacggaatttttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCAGGGTATCTTCATGCCTGTTTGAACACAGGGAAGCTTGCCTCCTTGGCAA
                     ttataac  putative branch site (score: 2)
                                           tttttgcttc  putative PPT
                     ttataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctcatttatcatgtatttattagagctgcttcttcatttagtattttattctgatctaatgcccttataacttggtgccaacggaatttttgcttcagTTATTACTCCCTATAACATGTGGCAGTGATTTGGAGATGGCAGACTTACCAGGGTATCTTCATGCCTGTTTGAACACAGGGAAGCTTGCCTCCTTGGCAA

- - - - - -catgtat
- - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgcc