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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttattccacaaactttgtgttttgcttttagccagtgcttttttattatgggagagaaggttttgttcaatatactggttttgtcattgattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAGTTGGAGAAGATTGGATATG

Basic information

species Glycine max
transcript GLYMA08G21290.1
intron # 2
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|26045900|gb|CA783324.1|CA783324
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|12774777|gb|BG239725.1|BG239725
EST:     GTTCCATTTACCAAGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCA
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCA
EST: gi|298198662|gb|HO042025.1|HO042025
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|192334789|gb|FK025280.1|FK025280
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|151411678|gb|EV281489.1|EV281489
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|17964059|gb|BM270800.1|BM270800
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298177612|gb|HO027279.1|HO027279
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGC
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGC
EST: gi|19346977|gb|BM891857.1|BM891857
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|24136066|gb|BU926576.1|BU926576
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298171957|gb|HO021549.1|HO021549
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|7042352|gb|AW472246.1|AW472246
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298167187|gb|HO010626.1|HO010626
EST:     GTTCCATTTACCAGGCACCGCAACTGTGTAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|192334790|gb|FK025281.1|FK025281
EST:     TTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: TTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|192307836|gb|FG999315.1|FG999315
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAA-G
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298187896|gb|HO031853.1|HO031853
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTAGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|19346603|gb|BM891483.1|BM891483
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298167682|gb|HO012945.1|HO012945
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTC
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTC
EST: gi|192330592|gb|FK022261.1|FK022261
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
EST: gi|298188965|gb|HO035658.1|HO035658
EST:     GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATT                         GGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG
genomic: GTTCCATTTACCAGGCACCGCAACTGTGCAATGTTTTTGCCGCCAGAATTgtgagatcat ... gattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatgggagagaaggttttgttcaatatactggttttgtcattgattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAGTTGGAGAAGATTGGATATG
                                         cattgat  putative branch site (score: 4)
                 ttttgttcaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttattccacaaactttgtgttttgcttttagccagtgcttttttattatgggagagaaggttttgttcaatatactggttttgtcattgattttgcagGGAAGGGCCCTTTATTACATACAAAAGGCTTTTACTACAGCTGCCTCAAAGTTGGAGAAGATTGGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA