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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcaaaaaccattatttaaaatgttaaaatctccatttatttttgcagtttatcttagcatcttttattgcacaaatttccatttttttttatattaattctgcacgcctggctgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGATATCAAAGATGCTACTGGTATTGAGGACAAGGAACTCAGAAGGACTCTGC

Basic information

species Glycine max
transcript GLYMA05G27240.1
intron # 12
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|16344341|gb|BI969936.1|BI969936
EST:     AGGCAGAGTTTNNNAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
EST: gi|12773136|gb|BG238063.1|BG238063
EST:     AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
EST: gi|31471408|gb|CD413436.1|CD413436
EST:     GTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: GTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
EST: gi|19346215|gb|BM891095.1|BM891095
EST:     AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
EST: gi|31561323|gb|CD487161.1|CD487161
EST:     AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
EST: gi|7686211|gb|AW756922.1|AW756922
EST:     AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG                         ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaa ... tgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacaaatttccatttttttttatattaattctgcacgcctggctgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGATATCAAAGATGCTACTGGTATTGAGGACAAGGAACTCAGAAGGACTCTGC
                        tattaat  putative branch site (score: 2)
                                            ctgtcctcc  putative PPT
     aaatttccattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcaaaaaccattatttaaaatgttaaaatctccatttatttttgcagtttatcttagcatcttttattgcacaaatttccatttttttttatattaattctgcacgcctggctgtcctccagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGATATCAAAGATGCTACTGGTATTGAGGACAAGGAACTCAGAAGGACTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA