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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaaatttagtacaaaacctgttcaaaattcaaattgccattcatgcatcttactctctgggaagtccttttctcaaacaacatcctcttattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATTTTAAACGAAGAGCAAGAGAATGAACTCCCTAACTTCCCATCATTCATTC

Basic information

species Glycine max
transcript GLYMA12G00600.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 2
-tccaaatttagtacaaaacctgttcaaaattcaaattgccattcatgcatcttactctctgggaagtccttttctcaaac-aacatcctcttattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATTTTAAACGAAGAGCAAGAGAATGAACTCCCTAACTTCCCATCATTCATTC
 |     ||||  |   ||  || |       ||   | | | || |    | || | |   || |   |  |||| | ||  |  |    | |||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||| |||| ||||| ||||| |||||||| || || || |||||||||||||
attggggtttatgaatgaa--tgctagttgcccatggttctactcttttcccctaattttgtggtatcacaattctgatactgatgtttcttaattttgtagGTTCGCAGGCTGAGGATACAACAAAGAATTAAAAGTGCTGAACTTGGAATTCTAAAAGAAGAACAAGAAAATGAACTTCCAAATTTTCCATCATTCATTC

upper sequence: GLYMA12G00600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 1
---tccaaatttagtacaaaacctgttcaaaattcaaattgccattcatgcatcttactctctgggaagtcctt-ttctcaaacaacatcctctta--ttttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATTTTAAACGAAGAGCAAGAGAATGAACTCCCTAACTTCCCATCATTCATTC---
   |     ||||  |  |||   |  || ||| |   |  | ||  |||| | ||    | || |   || |  |||| | ||    |  |||||  ||||||||||||| ||||| |||||||| ||||||||||||| ||| |||||||||||| ||||   ||| || || ||||||||||  || || |||||||||||||   
ttcttttgctttatcattaaa---gcacagaatgc---tgtcaatctatgcttattggggtttgtggcatcataattcttatactggtttttcttaatttttgtagGTTCGCAGGCTGAGGATACAACAAAGAATTAAAAATGCTGAACTTGGAATTCTAAA---AGAACAGGAAAATGAACTCCAAAATTTTCCATCATTCATTCCAT
















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|120491443|gb|EH219610.1|EH219610
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|6566524|gb|AW234167.1|AW234167
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|7924908|gb|AW830934.1|AW830934
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|19269603|gb|BM885859.1|BM885859
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|18038871|gb|BM307165.1|BM307165
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|9819295|gb|BE554808.1|BE554808
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|13479753|gb|BG509096.1|BG509096
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|33389909|gb|CA853116.1|CA853116
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|298167160|gb|HO010599.1|HO010599
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|13480083|gb|BG509426.1|BG509426
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|33389270|gb|CA852477.1|CA852477
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
EST: gi|12689436|gb|BG155833.1|BG155833
EST:     AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAG                         GTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT
genomic: AGGACAACATTCGAAGTCGGAGGAACAAAATCTTCTTACACATGGAAGAGgtctcacctt ... tattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcttactctctgggaagtccttttctcaaacaacatcctcttattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATTTTAAACGAAGAGCAAGAGAATGAACTCCCTAACTTCCCATCATTCATTC
   atcttac  putative branch site (score: 3)
                                     catcctcttatttt  putative PPT
                                            ttattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaaatttagtacaaaacctgttcaaaattcaaattgccattcatgcatcttactctctgggaagtccttttctcaaacaacatcctcttattttgtagGTTCGTAGGCTTAGGATACAGCAAAGAATTAAAAGTGCCGAACTTGGAATTTTAAACGAAGAGCAAGAGAATGAACTCCCTAACTTCCCATCATTCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA