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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttaaaagaagagattctttgttttaatgtttcccattgtggctctaatcacacctctttctgaaatctgaatactccttaaacttttgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTACCTGGTTGAATTATTATGATGCCTCAGAATAGAATTGGTCCATTGTAAA

Basic information

species Glycine max
transcript GLYMA06G12130.1
intron # 10
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|208099385|gb|GD899278.1|GD899278
EST:     GGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: GGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|193568834|gb|FK524779.1|FK524779
EST:     TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAG-AGATGGATTATTTTGTA
genomic: TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|208196671|gb|GE001015.1|GE001015
EST:     AGGGGCATGACTTCCCTTTGTTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: AGGGGCATGAC-TCCCTTTG-TCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|193406952|gb|FK375211.1|FK375211
EST:     TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|7795996|gb|AW781393.1|AW781393
EST:     TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATGTGAAGAG                         GTGGAGACATCTGTACTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|193661618|gb|FK605176.1|FK605176
EST:     CTTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: C-TCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|193464810|gb|FK432332.1|FK432332
EST:     TCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: TCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|193453006|gb|FK418586.1|FK418586
EST:     TCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATCTTGTA
genomic: TCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
EST: gi|21602646|gb|BQ612977.1|BQ612977
EST:     TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGAAATCTGGTCTGAATCTTCCCGG-GGAGAAGATGGATTATTTTGT
genomic: TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCC-GGTGGAGAAGATGGATTATTTTGT
EST: gi|193731981|gb|FK667081.1|FK667081
EST:     CTCCCTTTGTCTTTGTTTCCTATTTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGT
genomic: CTCCCTTTGTCTTTG-TTCC-A-TTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGT
EST: gi|31475757|gb|CD417785.1|CD417785
EST:     TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAG                         GTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA
genomic: TCTCACATAAGAGGGGCATGACTCCCTTTGTCTTTGTTCCATTTGAAGAGgtacattttt ... tgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaatcacacctctttctgaaatctgaatactccttaaacttttgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTACCTGGTTGAATTATTATGATGCCTCAGAATAGAATTGGTCCATTGTAAA
 ctctaat  putative branch site (score: 3)
                                         cttttgcccttc  putative PPT
                                    ttaaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttaaaagaagagattctttgttttaatgtttcccattgtggctctaatcacacctctttctgaaatctgaatactccttaaacttttgcccttcagGTGGAGACATCTGTTCTGAATCTTCCGGTGGAGAAGATGGATTATTTTGTACCTGGTTGAATTATTATGATGCCTCAGAATAGAATTGGTCCATTGTAAA

- - - aaaagaa
- - - - - - - - - - - - - - - -gtttccc
- - - - - - - - - - - - - - - - - - - -ttgtggc