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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta...

Basic information

species Glycine max
transcript GLYMA02G39360.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta-----
 || |||||| | ||||||||||||||||| || ||||||||||||||||| ||||| |||||  | || || || |||||||||||| | ||  | |||||        | | |  ||  |   | | |    | |    |||     ||   | |||    | |  || |   | |||||   ||      |||  |      
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgta-----tatatacaggagcaacctgttagaactaaaacatatttcagta---caagt----cttttcttatctagattttttctaacacccttttttgtatag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtg--------gcattctttttctagaatattttatcatttttcatttttatcctgat--aatcccagttacccctgcctcactcaaattttcaatatagaaatttacta
 || |||||| | ||||||||||||||||| || ||||||||||||||||| ||||| |||||  | || || || |||||||||||| | ||  | |||||         | |      |  |||||   |  | ||| ||||| |   |  ||  |   |||    ||    ||  | | ||    ||||   |||||          
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggaccaacctgttagaac--taaaacatatttcagtacaagtcttttcttatctagattttttctaacaccctt---ttttttgtatag----------

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 5'ss of exon 14
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta----------------
 || |||||| | |||||||||||||| || || |||||||||||||| || ||||| |||||  | || || ||||||||||||||| | || ||||||||   |    |        ||| || || ||||||   |  ||||    | ||  |||   |  ||  | |  | |  | ||   |    | || | ||                 
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgta-tacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcaga-gcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 1
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgt---------ggcattctttttctagaatattttatcatttttcatttttatcctga---taatcccagttacccctgcctcactcaaattttcaatatagaaatttacta---
 || |||||| | |||||||||||||| || || |||||||||||||| || ||||| |||||  | || || ||||||||||||||| | ||  |||||||         ||    | |  |  | ||| |||| |  | | |  ||| || |         ||| | || | |  |   |   ||  || |    | | | | |||  |    
GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G111355_T02 (Zea mays), 5'ss of exon 5
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgt---------ggcattctttttctagaatattttatcatttttcatttttatcctgata---atcccagttacccctgcctcactcaaattttcaatatagaaatttacta--------------------------------------------------------------------
 || |||||| | |||||||||||| | || || |||||||||||||| || ||||| |||||  | || || ||||||||||||||| | || ||||||||         ||    | |  |  | ||| |||| |  | | |  ||| || |         ||| |  | | |  |   |  |||| || | |  | |  |  |||  |                                                                     
GGCTAACAGTGCCAAAACATGGAAGAAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagtaggagcacatacttaataattttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttt-tgtatttttgtttaggtcgatgatgccttccttacaaagtaaatggtcctctccttgcccccagttatgatctgtttatag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttc----atttttatcctg----ataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta-
 || |||||| | |||||||||||||| || || |||||||||||||| || ||||| |||||  | || || || |||||||||||| | ||  |||||||   |    |      | ||| || || |||||||     | ||| |  |     | | |  |  | |    |  ||  || | ||      | |     ||   || 
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgta-tacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 24
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaa--tatagaaatttacta-
||| ||||| ||||||||||||||||||||||| ||||| |||||||||||||||||||| || ||||||||||| ||||| |||||  ||||||| |||||||     || || ||  || |||| |  | |   | | || | |||    |    || |    |     | |  ||| ||     | |  |  | |     
AGCCAACAGCTCAAAAACATGGAAGGAAGTTTGCTTTGCCTGTGTTGATGCTGAGGAATTTCGCTTGGCTCAGATATGTGGGCTCAACATCATCATACAGgtggagg--ttcttttatcatttttttttctataatagtcttctgctggctctttttgt-atggatttggaagtggaatgttagggttttgtagctctgtcct

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 5'ss of exon 25
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgt---ggcattctttttctagaatattttatcatttttcattttt--atcctgataatcccag---ttacccctgcctcactcaaattttcaatata---gaaatttacta----------------
|||||| || || |||||||||| |||||||||||||||||| || ||| | |||||||| || |||||||| |||||||| || ||  |||| ||||||||   ||| |  |     ||   |||  ||     ||| ||   |  | |||||||    |||     || ||   |  | |  | |||| ||| |    |||||   ||                 
AGCAAATAGCTCTAAAACATGGAGGGAAGTTTGTTTTGCTTGCGTGGATACCGAGGAATTTCGGTTGGCTCAAATTTGTGGCCTTAAGATCATTATTCAGgtattggcttagtcaacataatgtatcatacagaatttaatggatgaaacctgatatcttcaggatcaacaccatgcctagttcatttttgaatttgaatgaaatgggctttttgtggctgtggaag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 12
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatt-tacta---
 || || ||  ||   |||||||||||||| || ||||||||||| || || || || |||||  ||||||| ||||||||||||||||| ||  | |||||     |   |||||      | |||   |||   |||    || ||||  | | |   | || ||| |  |   | | |   || |   |||  ||||    
GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggataggtttctgc----tgttacattttgcaattagcctcatgattttactacgcaaccatgcttttcattactatcatatgttctaatcgtactgaag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 12
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtg------gcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta
 || |||||| ||   || ||||||||||| || ||||||||||| ||||| || || || ||  ||||||| ||||||||||||||||| ||  | |||||       || ||||  | ||   | ||   |||| ||||| |   | | ||| | |||   |||   | | |||   | |  |||    | |    || | |  
GGCCAACAGTGCACGGACGTGGAAGGAAGTCTGCTTTGCTTGTGTGGATGCCGAAGAGTTTCGTCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatgaaaagccttctaatgcttcgacatccgatcagttttcttgagttttctgtttatcaaggtt---ctttccttgattag-tttgttgtttcatgatgtgc--

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 24
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggc---attctttttctagaatatttta--tcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta
 || || |  |||   || ||||||||||| ||||| ||||||||||||||||||||||| ||||| || || || || ||||| ||||||||  | ||||||     ||| |||||| |  |  | |||  | |||  | | ||   | |   |||||  || |      |    |   ||| | | |    ||  || |    
GGCCAATAACTCACGGACTTGGAAGGAAGTGTGTTTCGCTTGTGTTGATGCTGAGGAATTTCGATTAGCGCAAATCTGCGGTCTTAATGTCATTGTCCAGgtgattttattatttttcaaccaagtcttagatgattacttagttgactacctttaatc--agctgtgtaaggagaagaaaaaatctgatgcaagttatctg---

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttcatttttatcctgataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgcc