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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaatcttgtgaccttagaattctgtagtgtatttttatgaatttgatattgggtgttgagtaatttttgaattaaatattggatgctgaatttttagTTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAGCAAGAAATCTGCAAACTCCCAAGCCTCAACCAAGGGTTCTACTGCACAG

Basic information

species Glycine max
transcript GLYMA11G05560.1
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|193682130|gb|FK621268.1|FK621268
EST:     CAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTCAGTACAG                         TTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTCAGTACAAgtaatattat ... gaatttttagTTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAG
EST: gi|193712643|gb|FK650968.1|FK650968
EST:     CAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTCAGTACAG                         TTATTAAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTCAGTACAAgtaatattat ... gaatttttagTTAT-AA-TCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACG
EST: gi|151397172|gb|EV267045.1|EV267045
EST:     CAATGGATGAAACGATACTGCGATTCTGTCGATTTCGGCCTTCAGTACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTCAGTACAAgtaatattat ... gaatttttagTTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatattgggtgttgagtaatttttgaattaaatattggatgctgaatttttagTTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAGCAAGAAATCTGCAAACTCCCAAGCCTCAACCAAGGGTTCTACTGCACAG
 atttgat  putative branch site (score: 5)
                                                ttttt  putative PPT
           tgttgagtaatttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaaatcttgtgaccttagaattctgtagtgtatttttatgaatttgatattgggtgttgagtaatttttgaattaaatattggatgctgaatttttagTTATAATCCTCTGGAGAGGAGAGAGGTTTGCAAAGGAGGAAGAGAAACGAGCAAGAAATCTGCAAACTCCCAAGCCTCAACCAAGGGTTCTACTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - tcttgtg
- - - - - - - - - - - - -tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgct