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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatgtgtgctctaaaaagtaacttgcttctaccactttgtgaattactttttctattactagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG

Basic information

species Glycine max
transcript GLYMA12G02920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G02920.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G17330.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------tgtatgtgtgctctaaaaagtaacttgcttctaccact-ttgtgaattactttttctattac-tagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG
                          |  |  | | |  | ||   |||  | | |     |    |   | | | |  |||| ||   || ||| |  | ||   |     ||  | |  | | ||||||| || || ||| |  |||||   | |    ||||     ||||||||||||| || || |||||||||||||| |||||||| ||||| || ||||
gtcagtttccagctcctactttttactcaacatatccaatcaactataatgtacatgatttatcactacaattaagtcattctgttgtatataaatttgtgaacagaacaagtgtattc--tttccagGTTTTAAAGACGAATTAGCAGGAGTAGCACTCTGTGAGTCTCTTCCAGAATTTGGGGTAGTTCAAGATGCTGATCGCCTTGATGCAATTGGCGCCATAG

upper sequence: GLYMA12G02920.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 4
tgtatgtgtgctctaaaaagta-acttgcttctaccactttgtgaatt----actttttctattactagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG
   |||    |||||||||||   ||||| |  | |  |||     ||    |  |   || |||| |   | |    || |||  | |    | |||  |||||||||||| || ||| |  ||||   ||  ||| |||||     |||||| ||||| ||||| |||||||||||||| |||||||| |||||||| || |
--aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttttacaaactagt-tataacttacgtacaa--ttcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
















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|151398243|gb|EV268121.1|EV268121
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|208291345|gb|GE094567.1|GE094567
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAAGGGTTTCCAGAA
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAA-GGGTTTCCAGAA
EST: gi|7693079|gb|AW761177.1|AW761177
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGCCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|208296315|gb|GE089611.1|GE089611
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|298164120|gb|HO013765.1|HO013765
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|24135503|gb|BU926013.1|BU926013
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATACTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|58022079|gb|CX708820.1|CX708820
EST:     AAGATCATCAAAGGAATGG                         G-TTCAANGG-AGAAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGA
genomic: AAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAA-GGAAG-AAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGA
EST: gi|213611749|gb|DB958871.1|DB958871
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|208295162|gb|GE091285.1|GE091285
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|298177471|gb|HO023604.1|HO023604
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAGGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|193414153|gb|FK377853.1|FK377853
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCGAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|298168341|gb|HO014516.1|HO014516
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAGTGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|193436738|gb|FK400883.1|FK400883
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCGAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|193429874|gb|FK395536.1|FK395536
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCGAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|298190152|gb|HO032273.1|HO032273
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
EST: gi|298185748|gb|HO028059.1|HO028059
EST:     AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGG                         GTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT
genomic: AGTTCAGGAGGACAACAAGTTCAAAATTTTGAAGATCATCAAAGGAATGGgtgagtttga ... caatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactttttctattactagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG
                                      ctgcttcc  CT-rich tract
          tattactagaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatgtgtgctctaaaaagtaacttgcttctaccactttgtgaattactttttctattactagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT