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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacactccctttatgtaagttttctcttgagctgacacagatctaaatattgaactttttgcatctatcatttgacactcatttggtcatctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTCTGAGCAGGCCGCACTGCAGTGCCTAGGTTGTGTAAAGGCTAAAATACCT

Basic information

species Glycine max
transcript GLYMA03G36550.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 1
-atacactccctttatgtaagttttctcttgagctgacacagatctaaatattgaactttttgcatctatcatttgacactcatttggtcatctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTCTGAGCAGGCCGCACTGCAGTGCCTAGGTTGTGTAAAGGCTAAAATACCT
   |   ||  | | ||| | |      || |    |    | |  |  || | |  |       | ||  | ||  |  |  |  | |  | | | | ||||||||| |||| || |||| ||| || ||||| |||||||||||||| |||||||| ||| |  |||||||| |||||||||| ||||| |||||||||
ttcaacatctgtatctgttaatgagtggtttaaaacattgggtttcagctagtaatatccagatttatacaaattttctgttgtcggatt-tatattgcagGTATCGTATACAAAGCGATAGAAAAGTAGCTGTCTGTAGTGTACATCCATCTGAGCATGCCACTTTGCAGTGCTTAGGTTGTGTGAAGGCCAAAATACCT
















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|207822489|gb|GD795180.1|GD795180
EST:     GACGGCCATTTCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGNTAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
genomic: GACGGCCATTTCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
EST: gi|209724922|gb|BW669612.1|BW669612
EST:     GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
genomic: GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
EST: gi|6719579|gb|AW307226.1|AW307226
EST:     GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
genomic: GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
EST: gi|213588581|gb|DB957522.1|DB957522
EST:     GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGATAAAAAGGTTTGCTGTT-GTAGTGTACATCCTT
genomic: GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTT-GCTGTTTGTAGTGTACATCCTT
EST: gi|214008711|gb|DB988246.1|DB988246
EST:     GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
genomic: GATTTCCCGGAAACCGCCCCGTTAGACGGCCATTTCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC
EST: gi|208283483|gb|GE088973.1|GE088973
EST:     TCTTGCGCTACAAGTG                         GTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTGGTGTACATCCTTC
genomic: TCTTGCGCTACAAGTGgttagtattg ... tctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatattgaactttttgcatctatcatttgacactcatttggtcatctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTCTGAGCAGGCCGCACTGCAGTGCCTAGGTTGTGTAAAGGCTAAAATACCT
                                          tcatcttt  CT-rich tract
        aacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacactccctttatgtaagttttctcttgagctgacacagatctaaatattgaactttttgcatctatcatttgacactcatttggtcatctttggaagGTATCGTGTACAGAGTGATAAAAAGGTTGCTGTTTGTAGTGTACATCCTTCTGAGCAGGCCGCACTGCAGTGCCTAGGTTGTGTAAAGGCTAAAATACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG