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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgaattgtatatatgtctgtgcctatgcattatcttgacttagtttatcactttcttggagactcatgagcttactatggttcaaatttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT

Basic information

species Glycine max
transcript GLYMA11G05080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05080.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23242 (Selaginella moellendorffii), 3'ss of exon 1
aattgaattgtatatatgtctgtgcctatgcattatcttgacttagtttatcactttcttggagactcatgagcttactatggttcaaatttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT
                                   | | ||    ||  |   | | ||||| | ||||  |  ||    ||| |  | ||    || ||||| || |||||||| || |||||||||||  |||||||||| || || ||||| ||||| |||||||| ||     | |||
----------------------------------gtatggagc--gtcgaatccatgcttgg-gtctcacaa--ttctcttggattga-ttgctctgtagCCTCTTCTTCAAGCAAGAGATGGAGTTATCAGTAATAGGACTACAAAAGGCTGGCAAGACGTCCCTTGTCAACTCCATCGCT
















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|151410326|gb|EV280141.1|EV280141
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGG-AATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|16349420|gb|BI975015.1|BI975015
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|209716493|gb|BW676943.1|BW676943
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATG
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCC-TTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATG
EST: gi|193625198|gb|FK577382.1|FK577382
EST:     TGGGAAGCTTTTCTCAATTGGCTACGCAG                         CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: TGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|58023255|gb|CX709996.1|CX709996
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|254344316|gb|GR851119.1|GR851119
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|58016934|gb|CX703676.1|CX703676
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|151412616|gb|EV282428.1|EV282428
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|254344317|gb|GR851120.1|GR851120
EST:     TGGCTTCGCAG                         CC-TTTTTTC-AGCA-GAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: TGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|207732378|gb|GD708551.1|GD708551
EST:     AAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTACGCAG                         CCTTTTCTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: AAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|192323170|gb|FK017396.1|FK017396
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|298177742|gb|HO023761.1|HO023761
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|254335359|gb|GR846856.1|GR846856
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|57574961|gb|CX547936.1|CX547936
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|18733799|gb|BM527816.1|BM527816
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|151395085|gb|EV264956.1|EV264956
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|151401783|gb|EV271596.1|EV271596
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|298167845|gb|HO013108.1|HO013108
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|58023508|gb|CX710249.1|CX710249
EST:     -ACAAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: AAC-AAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|9203981|gb|BE330205.1|BE330205
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|192301117|gb|FG988012.1|FG988012
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATG
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCC-TTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATG
EST: gi|58022262|gb|CX709003.1|CX709003
EST:     -ACAAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CC-TTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: AAC-AAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
EST: gi|151409006|gb|EV278814.1|EV278814
EST:     GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAG                         CCNNNNNNNCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC
genomic: GAACAAAAGACAATGGGATTGTGGGAAGCTTTTCTCAATTGGCTTCGCAGgtaggcttca ... ttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatcactttcttggagactcatgagcttactatggttcaaatttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT
                                         aaatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgaattgtatatatgtctgtgcctatgcattatcttgacttagtttatcactttcttggagactcatgagcttactatggttcaaatttgattgcagCCTTTTTTTCAAGCAGGAAATGGAGTTATCTCTAATAGGACTTCAGAATGCTGGGAAGACTTCCCTTGTAAATGTAGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - -gtctgtg
- - - - - - - - - - - - cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgag