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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctctcaaattgttattttcttaaaaaaaattatatcataaatattaagtttacacattggaactttgttttgctgatgattggatgctcttgtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAACGTAATCCATAGAGATTTAAAACCAAGCAACCTGCTGCTAAACTCAAACT

Basic information

species Glycine max
transcript GLYMA12G07770.1
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|192315258|gb|FK009606.1|FK009606
EST:     TTCACCATATCATTCACTCCAATCAAAATCTGTCGGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|254338777|gb|GR847494.1|GR847494
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|19934570|gb|BQ079600.1|BQ079600
EST:     CAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: CAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|23734544|gb|BU765510.1|BU765510
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|6567222|gb|AW234833.1|AW234833
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCANAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|7590950|gb|AW706693.1|AW706693
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAGAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|19938175|gb|BQ081596.1|BQ081596
EST:     CAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: CAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|6666996|gb|AW278455.1|AW278455
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCACAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|16346173|gb|BI971768.1|BI971768
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|192304508|gb|FG996774.1|FG996774
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTAC-AGATTCTTCGTGGGCTTAAGTATATACATTCTGCAA-C
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|213591425|gb|DB959911.1|DB959911
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|9565343|gb|BE474852.1|BE474852
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|21889903|gb|BQ743116.1|BQ743116
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|16105043|gb|BI892783.1|BI892783
EST:     ATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
genomic: ATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC
EST: gi|209726888|gb|BW675328.1|BW675328
EST:     TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAA                         TACTTCTTGTACCAGATTCTTCGTGCGCTTAAGTATATACATTCTGCAGAC
genomic: TTCACCATATCATTCGCTCCAATCAAAATCTGTCAGAGGAGCACTGCCAAgtgagtgctc ... gtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttacacattggaactttgttttgctgatgattggatgctcttgtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAACGTAATCCATAGAGATTTAAAACCAAGCAACCTGCTGCTAAACTCAAACT
                        tgctgat  putative branch site (score: 3)
                                        ctcttgt  putative PPT
                 tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctctcaaattgttattttcttaaaaaaaattatatcataaatattaagtttacacattggaactttgttttgctgatgattggatgctcttgtacttgcagTACTTCTTGTACCAGATTCTTCGTGGGCTTAAGTATATACATTCTGCAAACGTAATCCATAGAGATTTAAAACCAAGCAACCTGCTGCTAAACTCAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT