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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataaagtggcatcaatatatatatatacatggagttggttcatatctcaacttacttttatgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

Basic information

species Glycine max
transcript GLYMA17G02580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
cataaagtggcatcaatatatatatatacatggagttggttcatatctcaacttactttt----atgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC-
  |    |   ||  |  |||      | ||||||   |    | ||| ||  ||  |||    ||||||  |  ||||   | |  ||||  |||||   |||| | || || | ||||| ||||||||||| || ||||||||||| |||||||||||||| ||  | |||||  |  |   || |  |||       |||| 
ggtctcatttgatttac-tatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatctta---cagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGTCT-CTTTGGTTTCTACAAATCACA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
------------cataaagtggcatcaat-atatatatatacatggagttggttc---atatctcaacttacttttatgtcttaatattgtagtaatggtttaac---tctta----ttacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
              |    ||   ||| |     || | | |||     || | |   | |     |   |   |  |     ||| ||    | |  | | |     || ||    || |||| | |  ||||  |||| ||||||||||| |||||||||||||| ||||| ||||| || ||  | |||||  | ||||| ||||||||||||| |||| 
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
--------cataaagtggcatcaat-atatatatatacatggagttggttc---atatctcaacttacttttatgtcttaatattgtagtaatggttta---actctta----ttacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
          |    ||   ||| |     || | | |||     || | |   | |     |   |   |  |     ||| ||    | |  | | |     || ||    || |||| | |  ||||  |||| ||||||||||| |||||||||||||| ||||| ||||| || ||  | |||||  | ||||| ||||||||||||| |||| 
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 6
cataaagtggcatcaatatatatatatacatggagttggttca-tatctcaacttacttttatgtcttaatat-tgtagtaatggtttaactcttatta----cagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
  |||| | || |   | | | | | |   ||   |   |||| |||||  |   | ||  |       || |  || | | |  |  || | | ||||    |||||  | ||  || |||||||||| ||||| |||||||| ||||||||||| || || |||||  | |||||| || | ||  | || ||||| ||     
-gtaaactagcgttgttctgtgt-tctctctgatctcacttcactatctttaacca-ttcaagacaaacatgtacgttgaacttttcaaattttcattaacagCAGAGGCGACGCATGATAACGCATGCCAATGCCAAGAGCAAAAGTGAGAAGTTCCCCCCACCTCATCAGGATGGAGCTATGGGTAACCCATTGGGATCCA---

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: 13113.m00244 (Oryza sativa), 3'ss of exon 8
cataaagtggcatcaatatatatatatacatggagttggttca-tatctcaacttacttttatgtcttaatat-tgtagtaatggtttaactcttatta----cagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
    || | || |   | | | | | |   ||   |   |||| |||||  |   | ||  |       || |  || | | |  |  || | | ||||    |||||  | ||  || |||||||||| ||||| |||||||| ||||||||||| || || |||||  | |||||| || | ||  | || ||||| ||    |
----aactagcgttgttctgtgt-tctctctgatctcacttcactatctttaacca-ttcaagacaaacatgtacgttgaacttttcaaattttcattaacaacagAGGCGACGCATGATAACGCATGCCAATGCCAAGAGCAAAAGTGAGAAGTTCCCCCCACCTCATCAGGATGGAGCTATGGGTAACCCATTGGGATCCAGTC

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g27020.1 (Oryza sativa), 3'ss of exon 7
cataaagtggcatcaatatatatatatacatggagttggttca-tatctcaacttacttttatgtcttaatat-tgtagtaatggtttaactcttatta----cagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
    || | || |   | | | | | |   ||   |   |||| |||||  |   | ||  |       || |  || | | |  |  || | | ||||    |||||  | ||  || |||||||||| ||||| |||||||| ||||||||||| || || |||||  | |||||| || | ||  | || ||||| ||    |
----aactagcgttgttctgtgt-tctctctgatctcacttcactatctttaacca-ttcaagacaaacatgtacgttgaacttttcaaattttcattaacagcagAGGCGACGCATGATAACGCATGCCAATGCCAAGAGCAAAAGTGAGAAGTTCCCCCCACCTCATCAGGATGGAGCTATGGGTAACCCATTGGGATCCAGTC

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
cataaagtggcatcaat-atatatatatacatggagttggttcatatctcaacttacttttatgtcttaatattg--tagtaatggtttaa---ctcttatta----cagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
      ||| |||     |||  || |  || |  ||| ||   | ||  |  ||| |  | |    | ||| ||  || | | | ||  |   |||||||||    |||||  | ||| || |||| ||||||||||| ||||| || |||||||||||||||||||| ||  | ||||||  |   ||  ||||  | || || |   
------gtgccatagcccataagtaaactcaggctgtttgtcactttcaaatgttattgct-taatatgatactgaatattgaggtttccaaatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
cataaagtggcatcaatatatatata-tacatggagttggttcatatctcaacttacttttatgtcttaatattgtagtaatggtttaactcttatta----cagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
   | ||   ||| | || |   |   |   ||    |     || |     |||| | | ||  || |||||||  ||  |     | |||||||||    |||||  | ||| || |||| ||||||||||| ||||| || |||||||||||||||||||| ||  | ||||||  |   ||  ||||  | || || |  |
-ccatagcc-cataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgata-ctgaatattgaggt--ttccaaatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
--------------------------------cataaagtggcatcaatatatatatatacatggagttggttcatatctcaa------cttacttttatgtcttaa-tattgtagta----atggtttaactcttat-tacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
                                  |  | |||||| ||    | |  ||| |  | ||||  |   ||||  |      |  | | || | ||||   ||    | |     ||  |||  ||||||| |||||| | |  |  |  |||| ||||||||||| |||||||||||||| ||||| ||||| || ||  | |||||  | ||||| | ||| ||||| | |||  
gtacattcctatatttatttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatctggaagggtgccaaatcttgtctcttggctaacacaattcttcatcttttctctcttatctacagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
-----------------------------------cataaagtggcatcaatatatatatatacatggagttggttcatatctcaactt-------------acttttatgtcttaa-tattgtagtaatggtttaactcttat-tacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
                                     |  | |||||| ||  | | |  ||| |  | ||||  |   ||||  || |             | |||  | ||||   ||  |   |  |  ||   ||||  | |||||| | |  |  || |||| ||||||||||||||||||||||| || ||||| ||||| || ||  | || ||  | || |||| ||| ||||| | |||  
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
cataaagtggcatcaatatatatatatacatggagttggttcatatctcaa--cttacttttatgtcttaata--ttgtagtaatggtttaact--cttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
     |||   ||||    ||      | | | ||    | | || |  ||  |  |||||   || |   |   ||||  ||||  |||   |  |||| |||||| | |  |  |  | || ||||||||||||||||||||||| || ||||| ||||| || ||  |||||||  |  ||||    || |||| | ||||| 
----gagtcttatcagc-catggtccaaaaggaagcccatac-taccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA

upper sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
---cataaagtggcatcaatatatatatatacatggagttggttcatatctcaacttacttttatgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
   ||| | ||||| || |||||  | | |  ||  |||||||||  ||      |   || ||  | || ||       | ||   |  | |  ||  ||||||  | || ||  |||| ||||||||||| |||||||||||||| ||||||||||| || ||| | |||||||| |||||||| || |||||||||||||
tttcatcatgtggc-tccatataattttgttgatcaagttggttctgatacttg-tagtttgtagattttgattgctgtcttatatctccatttctaa-acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaacttacttttatgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC
                                           ctcttatt  CT-rich tract
       ttacttttatgtctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataaagtggcatcaatatatatatatacatggagttggttcatatctcaacttacttttatgtcttaatattgtagtaatggtttaactcttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - -acatgga
- - - - - - - - - - - - - - - - - gttggtt