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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacctttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT

Basic information

species Glycine max
transcript GLYMA12G07070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38630.1 (Oryza sativa), 3'ss of exon 6
------------------------------gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacc---tttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT
                               | | | |      || | |     || ||     ||||  |  |     | ||| ||   |  |    | ||||    | ||   | | | | | | |  |||| || |||||  | || |||||||||||||||||||||||||| |||||||| || ||||||
gtacatcacagtttttatccttggtgttcattcataccgtatccccactttgaagttgtggtcaaatgctcagttttccctgaggattactagttagaagcttatttgtttcctgttcttgttatttctccagGCTGTCCCTACTGCGAAAGGCCAAGCACTGGCTGATGAGTATGGCATCAAATTTTTCGAAACT

upper sequence: GLYMA12G07070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g13530.2 (Oryza sativa), 3'ss of exon 5
gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacctttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT-------------------------------------
 |   ||   |     || |     |||     |  | || |     || |  |        ||  |    || ||||      |    | |      ||||||| || || || ||||| |||||||| |||||||| ||||| ||||| |||||||||||                                      
atggtatatagcgttatcttggggattactccagtcttcaaattattattttggacaccttttggcttaatttttaattggttgtattatattaacacagGCCGTACCAACTTCAAAGGGGCAAGCACTTGCTGATGAATATGGCATCAAGTTCTTTGAAACGGTTAGTTGTTAATCTGTTTTAATATCTGCGCTTCTGT

upper sequence: GLYMA12G07070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g13530.1 (Oryza sativa), 3'ss of exon 5
gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacctttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT
 |   ||   |     || |     |||     |  | || |     || |  |        ||  |    || ||||      |    | |      ||||||| || || || ||||| |||||||| |||||||| ||||| ||||| ||||||||||| 
atggtatatagcgttatcttggggattactccagtcttcaaattattattttggacaccttttggcttaatttttaattggttgtattatattaacacagGCCGTACCAACTTCAAAGGGGCAAGCACTTGCTGATGAATATGGCATCAAGTTCTTTGAAACG

upper sequence: GLYMA12G07070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G878008_T01 (Zea mays), 3'ss of exon 5
-------------------------gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgatt-----------ataatatacctttg----gctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT
                          | | ||| ||  |  | | ||||    |   ||  || | |  |||| || || |    ||| || |   ||           |||||| | |||       || |   |  |||| || |||||  | || || |||||||| ||||||||||| |||||||| || |||||||| 
gtacttgcctgaactcattgttctccttaaatctggctgttttcactctgcattacttgtttgaa-atctgca-gttagatgcttaattttcccccttcaattagttaaataataaatcttcctgctactattgctccagGCTGTACCTACTGCAAAAGGACAAGCACTTGCTGATGAGTACGGGATCAAGTTTTTTGAAACG

upper sequence: GLYMA12G07070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04200.t01 (Vitis vinifera), 3'ss of exon 5
---gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacctttggct--ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT
     |||| |        | | | |||     | |||| ||||| |     ||  | |||  |   ||| ||||  |   || | ||||       || || |||| |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||||
gaaccaacaacttctccatttcccgctccctcttttgcacgcatatagatcagt--gtttttcaccatttttgatcgt---atccttttgataaaccctcttcagGCGGTGCCTACCTCCAAGGGCCAAGCACTTGCTGATGAGTATGGCATCAAATTCTTTGAAACT

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|16344867|gb|BI970462.1|BI970462
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|27445922|gb|CA953045.1|CA953045
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|209706956|gb|BW653172.1|BW653172
EST:     TAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|208066512|gb|GD866031.1|GD866031
EST:     TAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|192297076|gb|FG992012.1|FG992012
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTC
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTC
EST: gi|193388206|gb|FK354337.1|FK354337
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|208313500|gb|GE116028.1|GE116028
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|26047352|gb|CA784170.1|CA784170
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|209706955|gb|BW653171.1|BW653171
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|12691483|gb|BG157819.1|BG157819
EST:     TTAACACAATACTGGTGGGGAACAAAGCTGATATGGATGACAGCAAAACG                         GCCGTGCCTACGTCCAATGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|151409664|gb|EV279472.1|EV279472
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
EST: gi|209723917|gb|BW671590.1|BW671590
EST:     TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGG                         GCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA
genomic: TTAACAAAATACTGGTGGGGAACAAAGCTGATATGGATGAAAGCAAAAGGgtaagcaaac ... ttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtcaggtttgaaatgtttctgattataatatacctttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT
                    ttctgat  putative branch site (score: 3)
                                    cctttggctttctttt  putative PPT
              aaatgtttctgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatccgggagcctcctctctcttatgtatgcatgcatacatgcatgtcaggtttgaaatgtttctgattataatatacctttggctttcttttaagGCCGTGCCTACGTCCAAGGGCCAAGCACTGGCTGATGAGTATGGGATCAAATTCTTTGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctttg