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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatagaactgctatatatagttaaaatgattgttataatcaatcttaatttgtgcaaagaataatgacccttttgaattatcttctttataatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTTACAACGAGAGCAACATAGATCCGACATTTGCACAACAAATGCAAGCATT

Basic information

species Glycine max
transcript GLYMA20G38590.1
intron # 3
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|8284065|gb|BE021624.1|BE021624
EST:     TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAG                         GTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
EST: gi|192327335|gb|FK017782.1|FK017782
EST:     TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAG                         GTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
EST: gi|192324513|gb|FK018699.1|FK018699
EST:     TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAT                         GTGGTCACACAATCGGACTGGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
EST: gi|16345381|gb|BI970976.1|BI970976
EST:     TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAG                         GTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
EST: gi|58019441|gb|CX706183.1|CX706183
EST:     TGCTTTCGCCAAG-AAAATTTCACTACCCAAGAACTTGTTACTTTATCAG                         GTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
EST: gi|41145684|gb|CK605895.1|CK605895
EST:     TGCTTTCGCCAAGAAAAATTTCACTACTCAAGAACTTGTTACTTTATCAG                         GTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT
genomic: TGCTTTCGCCAAGAAAAATTTCACTACCCAAGAACTTGTTACTTTATCAGgtaaaattaa ... taatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttgtgcaaagaataatgacccttttgaattatcttctttataatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTTACAACGAGAGCAACATAGATCCGACATTTGCACAACAAATGCAAGCATT
 tcttaat  putative branch site (score: 3)
                                    tcttctttat  putative PPT
                          ttttgaattatcttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatagaactgctatatatagttaaaatgattgttataatcaatcttaatttgtgcaaagaataatgacccttttgaattatcttctttataatgttcagGTGGTCACACAATCGGACTAGTTAGATGCCGTTTCTTCAGAGCGAGGATTTACAACGAGAGCAACATAGATCCGACATTTGCACAACAAATGCAAGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - -actgcta
- - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaccc