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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT

Basic information

species Glycine max
transcript GLYMA15G00250.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------------------caaattatatct-tctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                                                         ||   ||   || | || |||  |    |      | |      ||||  || | |  |          || ||   || ||  |  |    | | | |||||||| ||||||||||  ||||||||||||||||| || ||||||||||||||| || | || | ||| || ||||  || ||||||||||| || ||||
gtaggattgtacagtggtttgcgtgctccttattttgatagatcacatggctgctagcactctacccctctttccctttctatcatccttgctcagtatttgtttttttcactttactggatggcatctttaccatgaacttgatttgttatgtgcagCTTGGGGAAACCATTTATCCAATGAAGGAAGATTTCATTATGGTTCATTTGCAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAAACGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 11
----------------------------------caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                                     |||   | || |   || ||||         |   || | ||||  |||       ||   |  ||  |  || | |   | ||||| ||||| |||||||| |||| |||||||||||| ||||| ||| | |||||||| ||||||||| || | |||| ||| || ||||   | ||||||||||| |  || |
gtaatattctttttcatgcagtatatgtacttacgccattgagttttttttttttttgcga--ggttatgccattgagttttgttgtagttctattatatgttattcatagtcatcatcttgat-tctatgcagCTTGGAGAAATCATTTGCCCAATTAAGGATGATCTCATCATGGTCCATTTGCAGTATTCGTGCAGTCACTGTTGTACCTTTATGGTGTCTGGAAGACGCT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 11
----------------------------------------------caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctc---tatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                                               ||| ||||   ||    |  |  |    | | |   | |    ||| | |   || |  |   | |      |||| | |  |||| || |     || ||||||||||||||||| |  || |||||||||||||| || ||||| ||||||||| || |||| | ||| |||||||  || ||||||||||| |  ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaatactctaaagtatac--tcctgttcttctctcccaccctaagtctcttttttacatacttgaattttatattaattgggtaacaca--ttttaattttgtgcatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTGCAGTATTCATGTAGTCACTGCTGTACCCTTATGGTGTCTGGAAGACGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 11
---------------------------------------------------caaattatatcttctcacttattgcatttaacatttatatggggtttccttgag---tggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                                                    |||   |||  ||   ||| |  |    | | | | | |    ||| |||||    || | || |       | | ||        | |  | | ||| ||||||||||||||||| |  || |||||||||||||| || ||||| ||||| ||| || | || | ||| || ||||  || ||||||||||| |  ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaataaatactcaaaaaaagtatactcctgcttctctctcccaccctgtctcttt--tttacttgaattttgtatattgggcgacacatttaccgtgctctattttgtgtatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTACAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAGACGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
----------caaattatat-cttctcacttattgcat-ttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagct--tttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
          |    |||   ||  ||  ||  ||||| | | | |   ||    ||||  ||   |     |  |  | |  | ||  |||   |  ||   | | | |  |||||||||| ||||||   ||||||||||| ||||||||||||||||| |||||||||   ||||| ||||||||||  || |||||  |||| || ||||
gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
       || ||||| | ||  | ||||  ||  ||||   |   || |||            | |    ||| || | |    ||   | | | |  |||| ||||| |||||||| || ||||||||||||||||| |||||||||||||| |||   ||||  |||||    | ||| ||||| ||||| ||||| |
------gtaacttcttattt-ctccattccactattat---gatcttgctt------------ccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 13
caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagct------tttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
  |||  | ||||   |   ||     ||    ||| |||    |||  |    |     | |   |||| |  |||| |   |      ||| | |  |  |||||| ||||| ||||||  ||| |||||||| || ||||||||||| || ||||||| | | |||||||||||||| || || ||||| ||||| || ||||
gtaatattttctttctatgaatattgcttcctttttgtatatatttttttctcatttgttttgtt-tttcttgttaatcatattcacctgttttaccgattcccagCTCGGTGAGACCATTCACCCGATGAAGGAGGACTTTATCATGGTCCACTTGCAGCCTTCTTGCACTCATTGCTGCATACTGATGGTATCTGGTAATCGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------caaattatatcttc--tcacttattgcatttaac----atttatatggggttt-----ccttgagtggaaatagcaatttccttg-taataaagcttttgatctctatcc---agCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                 || || |  |||   ||  | | |   ||| ||    | |  ||     | |     ||||   || | | ||  || |  |         | ||||||||   ||  |   |||| ||||| | |||   |||||||||||||||||| ||||||||||||||||| |||   || |  ||||| |||| ||| ||||| ||||| || ||||
gtaacttctttacctttaagttttccctttattcgttaactttgtttcactgatactcttacctaatcttcatgcctttgttgaagaaagtgatattatcaaccccctaacttttgattgttactctgtagCTGGGTGAGATCATCCTCCCAATGAAGGAAGATTTCATCATGGTTCATTTGCAACATTGTTGTAAGCATTGTTGTACTCTCATGGTATCTGGAAATCGTT

upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 11
caaattatatcttctcact--tattgcatttaacatttatatggggtttccttgagtggaaatagcaatttcc-----ttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
    | | |  |  |||||  ||||  ||||     | | |     |||     | || || |  |||||||      || | || ||||| |  ||   | |||||||||||||||||||  |||||||||||||||||||||| |||||||| ||||| |||||||| |||||||| |||  ||| ||||| ||||| |||||||
--tttcaaacgtcttcactgatattatattttctcctgacac---ttttgaacaaatgaaagt--caatttctgtttgttcttatgaagctatctattcttctccagCTTGGTGAAACCATAAGCCCAATGAAGGAAGATTTTATAATGGTTCACTTGCAACATGCATGTACTCATTGTTGTCATCTGATGGTATCTGGAAACCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT
                                      ttttgat  putative branch site (score: 4)
                                            tctctatcc  CT-rich tract
                          ttgtaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaattatatcttctcacttattgcatttaacatttatatggggtttccttgagtggaaatagcaatttccttgtaataaagcttttgatctctatccagCTTGGTGAAACCATTTGCCCAATGAAGGAAGATTTTATCATGGTTCATTTGCAGCATGCATGCACTCATTGCTGTATTCTAATGGTGTCTGGCAACCGTT

- - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - -ttgagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg