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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgattttttgacttggaagacaacaacacattattattataatatggttcaaaacaatgactttttctttatgatgtgaactccattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAATCTGTTTCCACCCAGTGAGAGAAAAGGAATAGCAATATCAACACTGTGTT

Basic information

species Glycine max
transcript GLYMA02G39230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g06720.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtgattttttgacttggaagacaacaacacattattattataatatggttcaaaacaatgactttttctttatgatgtgaactccattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAATCTGTTTCCACCCAGTGAGAGAAAAGGAATAGCAATATCAACACTGTGTT
|||||        |   | |  |  ||    ||  |  |       ||||  || | ||  |     || |    |  ||  ||        ||  |||  |  |||||||| |||||||||||||| ||||||||||| |||||  || |||| |||  |||||| ||||| |   |    |  |||||  | || |
gtgagaatgcccctctttcgttaatcagatccatgtctt-------atatacttaagaatta-----ttcttacaacaattggatgctttcattgcagTGGTATAGAAGCCCTGGAAAGGAAGGCTCCCACTTCAATCCTTACAGTGATATGTTCCCAATCAGTGAAAGAAAGGCCGTGCTCACTTCAACTGTATGCT
















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|58014509|gb|CX701251.1|CX701251
EST:     TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCNTACAGCAAT
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
EST: gi|151393687|gb|EV263562.1|EV263562
EST:     TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
EST: gi|151407473|gb|EV277288.1|EV277288
EST:     TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
EST: gi|192305128|gb|FG994678.1|FG994678
EST:     TCATTAGATTCACTGCGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAA
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAA
EST: gi|46492770|gb|CN472326.1|CN472326
EST:     TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
EST: gi|151394272|gb|EV264143.1|EV264143
EST:     TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTG                         TTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT
genomic: TCATTAGATTCACTGTGCCATTTCCATTGTTTGTGTATCCAATTTATTTGgtgagtgatt ... cattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatatggttcaaaacaatgactttttctttatgatgtgaactccattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAATCTGTTTCCACCCAGTGAGAGAAAAGGAATAGCAATATCAACACTGTGTT
                                          ctccatttttt  CT-rich tract
                       tttttctttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgattttttgacttggaagacaacaacacattattattataatatggttcaaaacaatgactttttctttatgatgtgaactccattttttagTTTTCAAGAAGCCCCGGAAAGGAAGGCTCTCACTTCAATCCCTACAGCAATCTGTTTCCACCCAGTGAGAGAAAAGGAATAGCAATATCAACACTGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA