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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattgtcgcttggaacattcactctagattatgagtgcatgcagtgccttttgggaagacactgctggaatatgaacacttaatctatacttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCTACCAGAAATCTTTCCTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGT

Basic information

species Glycine max
transcript GLYMA07G09270.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09270.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 12
caattgtcgcttggaacattcactctagattatgagt-gcatgcagtgccttttgggaagacactgctggaatatg-aacacttaatcta----tacttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCTACCAGAAATCTTTCCTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGT
      |    || ||   |  ||     | | || |   |   ||     ||||  |  |    | ||||||||  ||    |||| |     | |||  |||||||||||||||||||||||||| || |||||||||||||||||||| || ||||||||||| || || |  |||||||| || ||||| ||||||||||||
------tgatatgaaatgctggctaatagtgaagaatcatacttagacatgtttgaaataatgaggttggaatatataatctctaattttagactcctttgtgcagGTTTGTCTTAACATTTGCTCTGGGGGCTGGCCCAGTTCCAGGTCTTCTCCTACCAGAAATTTTCCCAAACCGAATAAGGGCAAAAGCTATGGCAGTCTGT
















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|58018453|gb|CX705195.1|CX705195
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|192327720|gb|FK021355.1|FK021355
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTCCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|19346368|gb|BM891248.1|BM891248
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|8284412|gb|BE021971.1|BE021971
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|21256350|gb|BQ453238.1|BQ453238
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|151399677|gb|EV269548.1|EV269548
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|254339875|gb|GR858000.1|GR858000
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|58017137|gb|CX703879.1|CX703879
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
EST: gi|8284214|gb|BE021773.1|BE021773
EST:     CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCT                         GTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT
genomic: CTTGTATCAAACATGGGAGCTCAGTACTTTTCTGTTGGTGGCATGTTCCTgtgagtatgc ... cttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttttgggaagacactgctggaatatgaacacttaatctatacttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCTACCAGAAATCTTTCCTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGT
                                 acttaat  putative branch site (score: 4)
                                   ttaatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattgtcgcttggaacattcactctagattatgagtgcatgcagtgccttttgggaagacactgctggaatatgaacacttaatctatacttcatgcagGTTTGTCTTAACATTTGCTCTCGGAGCTGGCCCAGTTCCAGGTCTCCTTCTACCAGAAATCTTTCCTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGT

- - - - gcttgga
- - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaac