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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcgcttcctcccatttgcttcttcaattttccgttaacaattccagttgtatgtaattttgaagtcctctctctctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTTTGGTGCCGAGTGATTCCCACGCGCCGCATGCAAATCGGAAGCTGAAGAT

Basic information

species Glycine max
transcript GLYMA07G39380.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 1
----------------------------gtctcgcttcctcccatttgcttcttcaattttccgttaacaattccag--ttgtatgtaattttgaagtcctctctctctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTTTGGTGCCG--AGTGATTCCCACGCGCCGCATGCAAATCGGAAGCTGAAGAT
                             ||||||   |  ||   |||||  |   | ||| ||||    |   ||  ||  || | || | |  ||  |     |    |||||  |||||||||||||||||||| || |||||||| || ||||| | | |  ||||||||     |   ||  ||  |  || ||   ||  | |  |  |  
gtcagtcccgagcccgactcttctgtggatctcgccctcctcc---tgcttggttggtgttc-gttactggtgtgagctttagatttgatctggttgtggtggtggtggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGCTGGTGCCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCA-AGGTCGGCGT-
















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|254318249|gb|GR832417.1|GR832417
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
EST: gi|193570764|gb|FK529475.1|FK529475
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACC
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACC
EST: gi|207700556|gb|GD683663.1|GD683663
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
EST: gi|254323780|gb|GR836119.1|GR836119
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
EST: gi|213599182|gb|DB958401.1|DB958401
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
EST: gi|193388168|gb|FK353879.1|FK353879
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACC-TG                         AGGAGATCGCGAAGCTGTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTT
EST: gi|208194728|gb|GD989355.1|GD989355
EST:     CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTG                         AGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT
genomic: CCCTTTCATCATCGTCGACGGTCCCCAAAGCTCCGCCGCCGGCAACCCTGgtctcgcttc ... tctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgttaacaattccagttgtatgtaattttgaagtcctctctctctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTTTGGTGCCGAGTGATTCCCACGCGCCGCATGCAAATCGGAAGCTGAAGAT
   cgttaac  putative branch site (score: 3)
                                    tcctctctctctcttg  putative PPT
                  ttgtatgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcgcttcctcccatttgcttcttcaattttccgttaacaattccagttgtatgtaattttgaagtcctctctctctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTTTGGTGCCGAGTGATTCCCACGCGCCGCATGCAAATCGGAAGCTGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA