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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT

Basic information

species Glycine max
transcript GLYMA06G17140.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
------gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggacc-----atggattccactattaaagatgtacatggatattgtaacatgcactttta-tcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
       ||      ||  | |  | | |||  |      |     ||||| ||    ||  | |  |||  |          | |||||  |  | | | | |     || ||| | ||  |||    |    ||  ||  || ||| ||||  |  | |  |  | | |  || |||||||||||||| |||||  | || || ||||||||||| |  ||||| || ||||||||||| ||||| |||| ||| |||||||||||||| ||||| |
gtaatgatatattggtttatttgtcttcttacctgccaagtccttgtcactgttgtagctagtcatgattttagttc-cacaatagttttaagaaataggtagctcaggatagatcctacctttag---tccctatctattctgaaac-tgcatatgcaatggttatatgtctttacagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 3'ss of exon 2
-------gtaagaaatttagtgtaccat-tttaattttgt---tatttaaatcactat---------tagttcttttaagaattcaaacaaatt-ttgtggtttttggtgacaaggaccatggattccact-attaaagatgtacatggatattgtaaca-tgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
        |||     || |  |  ||  |||   |||||   | | ||| || || |         | |||   ||  || ||   ||| |   || | | | |    |  |||||  |   |||    | |       |   ||    |  || |  | ||   ||   |  ||| |  |  ||  ||||||| ||||| |||||  | |||||||| || ||||| || |||||||| ||||| ||||||||||| |||  ||| ||||| ||||| |||||||| |
gtgtgtgctaattcccttggcatctcacatttggatttgtctgtgtgtaattctctttctgatttcattgtttactttggagtttggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaagttctgaagtagtgttattaactgttgtatactatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACGTTGGTCCAAACATTTGGACAGGAGAACCATGTTTGCTTAAAAGAGGGTT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactat----taaagatgtacatggatattgtaacatgc--acttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                                         ||  |  | |    |||   | ||| |  ||   ||| |      |   | |   ||| ||||  | | |    |  |||  | | | || ||||| |||||||| || ||||||| | | ||||| || ||||||||||||||||| ||| ||||||| || ||||| || | ||| ||||| |||||||| || ||||
-------------------------------------------------------------------------ttaatcatctaccctgattggcaccttctatcatactttgtgcccacattctctttggttatttcagcgtattgatcttttgcttctgttattgtttcagGAAGAAAAGGCAATTGGACGTGGAATCCTCCCATTGCTTCAGCGTGCCACCCTGGTTCAGACCTTTGGACAAAAGAACCATGTCTGCTTGAAGGACGGCT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                      ||||  |    |||| | |       |||    |    |  ||  |   |  |  | || || || |  ||   |  ||||||| | ||||  | |         ||| ||||||||||||||| |||| | | ||||| ||||| ||||||||||||||||| |||||||| || ||||| |||| ||| ||||| ||| |||| || || |
------------------------------------------------------tttagtagaaaaaaccactcactaaatttccaat--tgactactgttactgtctgt-ttcaatatcttgatattt-ctgtaacaagtacttcaaac---------tgtaccagGAAGAGAAAGCCATTGGACGGGGAATCCTTCCCTTGCTTCAGCGTGCTACGTTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGATGGGT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                           ||  |  | ||   ||| |  || |  |       | |  |  || ||   | | |   | |||    |  |||||   ||       ||  | |     | ||||||||||| ||||| || ||  | ||||||||||||||||| |  |||||||| ||||| ||||| ||||| |||  ||||||||| ||| |||| ||||| |
---------------------------------------------------------gtgaggttcaccatgcttt-tcattgtgtgcagtcttgccttttaatgccttaacttacattttactcacaagttgta---tgtgtaacgattgtatcggcat-ttccagGAAGAAAAAGCTATCGAGCGTGGAATTCTTCCATTGCTGCGACGTGCTACATTGGTCCAAACCTTTGGACAGGAGAATCATGTTTGCCTGAAGGAGGGTT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattcc--actattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                             ||    |||| ||       ||   ||     | ||| |  ||| |   || ||  |      |     |  |||||||    |  ||  ||  || ||||    ||||||||||||||||| |   | ||||| ||||| |||||||||||||||||  ||||||| || ||||| |||| ||| ||||| ||| |||| |  || |
------------------------------------------------------------tataatgacaacttgctaaacttccagttg---gcaccttacattactggctgttccaacatctcgatatttctgtaacacaagcgctt--caaattatttt----cagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGCGGGT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G141094_T01 (Zea mays), 3'ss of exon 7
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttgg-tgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                   |  | | | |||    |||| ||||   |||      | |||   ||      |||||  ||    ||| |       |  |||||||    |  ||  ||  || ||||    ||||||||||||||||| |   | ||||| ||||| |||||||||||||||||  ||||||| || ||||| |||| ||| ||||| ||| |||| |  || |
---------------------------------------------------tactgttataat---gacaacttttccagttggcaccttacatttactggctgttccaacatctc-gatat-------ttctgtaacacaagcgctt--caaattatttt----cagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGTGGGT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 9
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                 || || |||  |      |||| ||||   |||   ||   |    |  |  |  |   | |  | |  |  | ||   | ||||||||    |  ||  ||  || ||||    ||||||||||||||||| |   | ||||| ||||| |||||||| ||||||||  ||||||| || ||||| |||| ||| ||||| ||| |||| |  || |
-------------------------------------------------gtactgttataat----gacaacttttccagtt---ggcaccttacattactggctgttcca--acatctcgatat---ttttgtaacacaagcgctt--caaattatttt----cagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAACGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGTGGGT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                       || |     || | || |||   |     ||   |||| ||     |  |    || |    |  ||  ||              | ||| | |  |||||   |||  ||||||||||| ||||| | ||||||||| || || |||||||| || |||||  |||| || |||||||| || ||||||||||| ||||||||||| || |
-------------------------------------------------------ttgatggagcagaaaattttcacgagccgtgacaacaaagatttgtgcctgtgatactgctaacctagctgat------------ctcttgttttgtgtttgactgtggcagGAAGAGAAGGCAATAGGAAGAGGAATACTACCCTTGCTTCAACGAGCTACACTGGTGCAGACATTTGGACAAAGGAATCATGTTTGCTTGAAAGAAGGTT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtaagaaatttagtgtacc---attttaattttgttatttaaatcact---attagttcttttaagaattcaaacaaattttgtggtttttggtgacaa--ggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                   |  |  |   |||   ||   |  || |||   ||   ||     ||   ||  | ||||  |  || |    || |||| ||  ||    | | |    ||    ||  ||    |  ||||    |   |    | | | ||  |  || |  ||||||   ||  |  |||||||||||||| |||||||||||||||||||  ||||| |||||||| |||||||||||||| ||||| ||  |||||||||| ||||||||||| ||||
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcat---tattcactttcactgggcctctgttcatgtccatt-ataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT

upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 2
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                                                            ||| | |   |||  ||      || |     |  |  ||   ||  ||| |   |  |   |||   |    |     |   |       ||||  | |  |  ||||||||||||| |||||| | || ||||| ||||| || || ||||| ||||||||||| || ||||| || ||||| |||||||||||||| ||||| |
------------------------------------------------------------aatgcga---aatcctgcctacatttgaattgaaaaatattcgttgtacttt---atcttggcataactcacatg-tgagtgttccatctttgttcgtattgtgtagGAAGAGAAAGCTATTGAACGGGGGATTCTCCCATTACTCCAACGTGCAACCTTGGTTCAGACTTTTGGACAAAGGAACCATGTGTGCTTGAATGAGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
                  ttgtaac  putative branch site (score: 2)
                                       tgtttttttgttcc  putative PPT
                               ttttatcatgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgacaaggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG