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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

Basic information

species Zea mays
transcript GRMZM2G086994_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
gtatgagaattctcctatggatgtgcttctttgta-acat-ttttaactgtttttgggaaaaaa--tttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
|| ||| |  |||| ||      ||||| ||  || || | ||||  |||||||    || | |  ||   |  ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| ||||| | ||||
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
gtatgagaattc-tcctatggatgtgcttctttgtaacattttta------actgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
||||||   ||| |  |     | ||||  |   |   |  |  |      | ||   ||||  |||   |  | ||  |  ||  |||||||||||||| |||||||||||| |||| || ||||| ||||| ||||||    | |||||||| ||||||||  ||  || ||| |   |  |  |  
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgcaattggttaaaccatgccttttgtttaa-acagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
gtatgagaattctcct-atggatgtgcttctttgtaacatttt-------taactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
|| |||   ||||  |      | ||||  ||  |   |  |        ||| |||  |    |||  ||     ||  | |||  ||||||||||||||||||||||||||| | || || ||||| ||||| ||||||    | |||||||| ||||||||  ||  || ||| |   |  |  |  
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttgtttaaa--cagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G28820.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                                            | |||   ||||  | ||  |     || | | || ||||| | | |  ||||    ||  |||| |   |||| |  ||||||||||| || || ||||| ||| |||| || || ||||||||||||||| | || |||||||| ||||||||||    || ||| || |   |  | |
gtctgtatcactttttgtatttactacataaggctaggcatgcttttgaatgttctgttttgttttctgatcatggaaatattttgatccgagtttg----aatgtttataaatatgata-acagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCATCCAAATTCCAC

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                                         | || ||||| |  | |   | |  ||| |    |   |   |  | | ||        ||||| | |  |||| |  |||||| ||||||| || ||||| ||  |||| ||||| || |||||||||||| | || |||||||| ||||||||| |   ||  ||  | |  ||     
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactct-tttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgata-acagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                                         | || ||||  |  | |   | |  ||| |    |   |   |  | | ||        ||||| | |  |||| |  |||| ||||||||| || ||||| ||| |||| ||||| || |||||||||||| | || |||||||| || |||||| |   ||  ||  | |  |      
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactct-tttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgata-acagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G10230.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                                               | |||   |||   | ||  |        | | || ||||| | |||  ||||       ||  |   |||||| |  ||||||||||| || || ||||| ||| |||| || || ||||||||||||||| | || |||||||| ||||||||||    || |||  | |   |  |  
gtctgtgtcacttttttgaatttacttacataaggctaagagtgttttgtgaatgttcagttttgttttctgacagtggaaagattttgatctgaatttgaatgtttataaatgataatgata-acagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCGTCCAAATTCCAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G02540.1 (Glycine max), 3'ss of exon 4
gtatgagaat----tctcctatggatgtgcttctttgtaacatttttaactgt---ttttgggaa---aaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
|||||| |||      || | | | | | |||||   |  | |  || || |    || || ||    ||    | | ||      |  |||| |||||||||||||||||||||| |||| || ||||| ||||| | ||||    | |||||||| ||||||||  ||   |  || |   |  |  |  
gtatgataatggcacttctttttgctcttcttctccctcgcgtaattgacagcaaattatgcgatgttaagccatgccttttgtttaaacagGATGAGAAAGAATGCTCCTACTATTTGAAAACAGGGCAGTGCAAATATGGTATATCTTGTAAATTCCATCATCCTCAACCGGCGGGCACATCATTGCCAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
gtatgagaat----tctcctatggatgtgcttctttgtaacatttttaactgtttttgg------gaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
|||||| |||      || | | | | | |||||   |    |  || || |    ||       |  ||||  | | ||      |  ||||||||||||||||||||||||||| |||| || ||||| ||||| ||||||    | |||||||| ||||||||  ||   | ||| |   |  |  |  
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
    |  |  | |  |     |    |    |  ||   |  |  |   |||   | |  |  ||  || ||     || ||||||| || ||||||||||||||| |||| || ||||||||||| ||||||   || |||||||||||||||||  |   || ||||| | | ||  | |
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC------------------------------------------------------------------------------
    |  |  | |  |     |    |    |  ||   |  |  |   |||   | |  |  ||  || ||     || ||||||| || ||||||||||||||| |||| || ||||||||||| ||||||   || |||||||||||||||||  |   || ||||| | | ||  | |                                                                              
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtatgagaattctcctatggatgtgcttctttgt--aacatttttaact-gtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                                         || | |  |       |||| |||  ||         ||| ||  |  | | || ||   |  ||||   | |  || ||  ||||||||||||||||||||||||||| |||| || ||||| ||||||||||||   ||||||||||| ||||||||  ||   | ||| |   |  |  |  
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttgggaatggacacttccatttagcttatgtttatgaattggaaattttgcaa--cagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG

upper sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g01650.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtatgagaattctcctatggatgt--gcttctttgtaacatttttaactgtttttgggaaaaaatttacattaa----tgaaatg------cagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                    | |   |  | |||| |  ||||  | ||  ||| ||     |   |||   || | |   || ||   | ||    ||| |||      |||||||| ||||| |||||||||||| ||||||| || |  ||||||||||||   ||||||||||| ||||||||| |    | | | || |   |  |  
gtctgtgtttgttgcaactttttttaatctatcctgttaatgttagatttattggaatcacatagcctgaagtttgcagttaagttggctcaaagcttgatatgttgctacagGGTGAAAAAGAGTGCTCCTACTATGTGAAGACAGGACTTTGCAAGTTTGGTGAAACATGTAAATTCCATCATCCACAGCCAGATAGCATACAACTGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
                             aaaaaatttacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG