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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttctctttctaaggtggattatttgcttcagcagtcaattttctgactgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG

Basic information

species Glycine max
transcript GLYMA06G13330.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
----gtaattcttctctttctaaggtggattatttgcttcagcagtcaatt-ttctgac--tgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
    | | | ||    | ||| | |  || | |    |  ||  ||   || || | |     | | |   ||    ||| |  |  ||||| || ||||  || ||||| ||||||||| |||| || ||||| ||||||||||| |||||  | |||||||||||||||||||| |||
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG

upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 19
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 18
---gtaattcttctctttctaaggtggattatttgcttcagcagtcaattttc--------tgactgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
     ||||||    | | | |    ||||      |||||   | | ||||          | ||||   ||| |||  ||  ||| |  ||||| || ||||  |||||||| ||||||||  |||| || || || |||||||| || |||||| | |||||||| ||||||||||| |||
gcaagaattctctgatgtttgaacgagattggaatgttcaggttttattttttgatattatcggctgtaacatgtgtatgtttaatg-taacagAGGACAGAAATGGATCGGGTCTGCTTTGGGCGATCTGGAATTCATGGATGGGGTCTTTTTGCAAGAAGAAATATCCAAGAAGGAGAAATG

upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 19
----------gtaattcttctctttctaaggtgg----attatttgcttcagcagtcaattttctgactgttttatgggtactt-tgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
           | |||  | |    | |   |      || |  | |||     | | ||||| |   | |||| |  | | |  |  | || ||||||| || ||||||||| ||||||||||||||||||| || ||||| || |||||||||||||||||   |  ||||||||||||||| |||
gtaaattttcatcatttctgttcagcaattatcctcctatcaacttcttggattgacgatttttttttttttttgtatgcattcatacacgactccagAGGACTGAAAATGATAGGGTTTGCTTTGGTAGATCTGGAATACATGGCTGGGGCCTCTTTGCACGACAAGCTATTCAAGAAGGAGATATG

upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ23651 (Selaginella moellendorffii), 3'ss of exon 10
gtaattcttctctttctaaggtggattatttgcttcagca-gtc-aattttctgactgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
                               | |  | || ||| || ||||       | |||| |  |  ||  || | | ||| ||| || ||     | ||||||||||||| ||||||||| || |||||||| ||||||||  |  || | ||  |||||||||| |||
-------------------------------gttcgaacacgtctaaatttccaggatatatatgtg-gccgtgcctggtgc-agAAAACTGAGAAAACGAGAGTTTGCTTTGGTAAATCAGGCATCCATGGATGGGGACTCTTTGCGAGGCGATACATCAAAGAAGGAGAGATG

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|16105061|gb|BI892801.1|BI892801
EST:     ACGAACCTCAGGCATTTTCTTCTTTCAGAGAACGCCTATACCACTTGCAG                         AGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGG
genomic: ACGAACCTCAGGCATTTTCTTCTTTCAGAGAACGCCTATACCACTTGCAGgtaattcttc ... atgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGG
EST: gi|27808927|gb|CB063349.1|CB063349
EST:     ACGAACCTCAGGCATTTTCTTCTTTCAGAGAACGCCTATACCACTTGCAG                         AGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGG
genomic: ACGAACCTCAGGCATTTTCTTCTTTCAGAGAACGCCTATACCACTTGCAGgtaattcttc ... atgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttcagcagtcaattttctgactgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG
                   ttctgac  putative branch site (score: 2)
             tcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcttctctttctaaggtggattatttgcttcagcagtcaattttctgactgttttatgggtactttgtatgattccagAGAACCGAAAATGATCGGGTTTGCTTTGGTAGATCAGGCATACACGGATGGGGCCTCTTTGCACGTAGAAATATTCAAGAAGGAGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA