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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag

Basic information

species Glycine max
transcript GLYMA06G04390.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatatt-cacttaca--cactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag----------
||||||||| ||||| || || |||||||| || ||| | || || ||||||||||| |||| |||||||||   |||||| |||||||||||||| ||||||    ||| |  |      ||     ||| |   || |   |  |||  |      ||||  |||    |  |      |  |          
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatgg--aatgacgaccgtgatggtgtgtcgcgtgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os09g28200.1 (Oryza sativa), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag------
||||||||| ||||| || || ||||||||  | ||| | || || ||||||||||| ||||||||||||||    ||||| ||||||||||||||||| |||    |  | |     | | |  |   ||  ||| ||| |        ||   |||  |     |||   | |   |         
CTTCGTCGTGTGGCGGCCGCCGGAGTTCGCGCGCGACATCCTCCCCAACTACTTCAAGCACAACAACTTCTCGTCGTTCGTCCGCCAGCTCAACACCTACgtaagcaaagcgccatgccgccaccttctgtagttctgttctctcgtgcgttttgatgcgtgtaagtaacgacgtcgttgcaatgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G088242_T01 (Zea mays), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgta--ttatattcacttacacactatatctagttcttcagttattcttataattaacatggtta-attttaaatgcatgaattag--------------------------
|||||| || ||||| || || ||||||||  | ||| | || || ||||||||||| ||||||||||||||   ||||||||| ||||| |||||||| ||   |    ||| |       ||   | ||| |   |  |             | |  ||    ||  | |  ||  |     |                          
CTTCGTGGTCTGGCGCCCGCCGGAGTTCGCGCGCGACATCCTCCCCAACTACTTCAAGCACAACAACTTCTCCTCCTTCGTTCGACAGCTAAACACCTACgtgagtcgccttcgcacttggccttggtttagctaagccttggaggccgcgcggagcgcggacggatggtgaccgccggtgacggcaatgctgcaacgggcaataatgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G46264.1 (Arabidopsis thaliana), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagt-tcttcagttattcttataattaacatggttaattttaaatgcatgaattag--------------------
 || |||||||||||||| || ||||| ||  | || ||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||| || |||||||    |  | | |  | || |   |  | |||  |||||   || | |||| ||     | ||    ||    || || |                    
TTTTGTCGTTTGGCGTCCACCGGAGTTTGCTCGTGATCTTCTTCCTAATTACTTTAAACATAACAACTTCTCTAGCTTCGTTCGTCAGCTCAATACTTATgtat---gtagaataaagctctctcctttctctctaaagttacgatttttattaccaaaacgatttgggtatttgagattttggtctgttatacgttttttgt

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g10380.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtat-tatattcacttacacactatatctagttcttcagttattcttataattaaca-tggttaattttaaatgcatgaattag-----------------------------------------------------------
|||||| || ||||||||||||||||||||  | || || ||||| || ||||||||||||||||||||||||||||||||  | |||||||||||||||||||   |  || ||    | | |  ||   |  |  | |  ||  |  |  |   | ||||||  | || ||  |||||  |                                                            
CTTCGTGGTGTGGCGTCCTCCTGAGTTCGCTCGCGATCTCCTTCCCAATTACTTCAAACACAACAACTTCTCAAGCTTCGTCAGACAGCTCAACACCTATgtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttat---tcttataattaacatggttaattttaaatgcatgaattag---------------
||||||||||||||||||||||||||| || ||||| ||  | || ||||||||||| |||||||| || || |||||||| || || || ||||||||||||   |   || ||  |||| |  |  | |  |    |       ||     ||||| |       | ||||||    ||                   
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaatgagacaaccgatcagataaaggagga

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S12_41V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgta----ttatattcacttacaca-ctatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaa-ttag---------------
 |||||||| |||||||||||||| |||||  |||| ||| | || || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||||        ||||  || | || || | |  | | | | |   |||    |||||  | |    |||    ||| ||| |  ||||               
ATTCGTCGTCTGGCGTCCTCCTGAATTCGCTCGAGATCTTTTGCCCAAATACTTCAAGCACAATAACTTCTCTAGCTTCGTACGACAGCTGAATACCTATgtaagctccgcattccgtttcgcaactgtgttgattgcgtgaa--atttgattaattgccgtc-caaatgagtaatacatcaggttagtcaaagagaatgaat

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S19_153V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcactt-acacactatatc-tagttcttcagtta-------ttcttataattaa-catggttaattttaaatgcatgaattag---------
||||||||||||||| ||||||||||| || ||||| ||  | || ||||| ||||||||||||||||| || ||||| || || || || || || ||||||   |   || || |||||  ||||  |  |  ||||| |         ||  |||  |||  |  |||    | | | |   || | |          
CTTCGTCGTTTGGCGCCCTCCTGAGTTTGCGAGAGATCTCTTACCCAACTATTTCAAACACAACAACTTTTCCAGCTTTGTGCGACAACTAAATACTTATgtaagctccgcattttacacaa-atatgatgataattcagatggagcgttctcacatagctaagtagcgtttcagtgagaagtgcgattcactcgaggaag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S207_20V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtat-tatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag-----------------
|||||| || ||||| || || ||||| ||| | ||| | |||||||| |||||||| ||||| || ||||| ||||| ||| | |||||||||||||| |||  |  || ||||||       |    |  | |   | |  ||      | |  | ||| || ||| ||  |  |  |                    
CTTCGTGGTCTGGCGACCGCCAGAGTTTGCACGGGACTTGCTTCCTAATTACTTCAAGCACAATAATTTCTCCAGCTTTGTTAGGCAGCTCAACACCTACgtaagtcgatccacttaagggacgttgtaaaatatcaggatgatcgagatttgagaaaggtgaaatttgaaaactaggctcgagaagacaccagggttgg

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ15796 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaa--tgcatgaattag----------------------------------------------------
 ||| |||| ||||| || || || ||||| |  ||  |  | || || |||||||| ||||| |||||||| || ||||| || |||||||||||||| ||        ||        || |    |  || |||    |  ||  | || |     ||| || |  |  ||||  | | ||                                                    
GTTCATCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcgcatacgttttctttccacacctcctcatagttctttggagttcagtcccttagttcttcacttgcagtactcagcttcagctgtcaatgatgttgcccactgaacttcgttcttgtcgactcgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ31857 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgta--ttatattcacttacacactatatctagttcttcagtta---ttcttataattaacatggttaatt-ttaaatgcatgaattag-------------------------------------------------------
 |||||||| |||   || || |||||||| |  ||  | || || | ||||||||| |||||||||||||| |||||||| || ||||||||||| |||||   ||  ||||          | | |    |   ||  ||    ||| |||  ||  |  | |         |  |  ||  |                                                          
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgtttgcttcgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ28850 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag
||||||||| ||| | || || ||||||||  | ||| | || || ||||||||||| |||||||| ||||| |||||||| || |||||||||||||||||     | || ||  |  |  |  |  |     ||| || ||||   |  | |     |||   |    | | || |    
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtg----agtctct--cgaatcaccttgaagctctcacttgttctccgatctgatcatcttatcgtcgcgttcttgcag---

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ38003 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtat-------------------tatattcacttacacactatatcta---gttcttcagttattcttataattaacatggttaattttaaa---tgcatgaattag---------------------------------------
 |||||||| |||   || || |||||||| |  ||  | || || | ||||||||| |||||||||||||| |||||||| || ||||||||||| |||||                     | | |||  |  | | || |  ||     |  |||  |  |||||  |   | | |  ||   ||| |    |||| || |                                          
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgt--tttgctttgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ17520 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag
||||||||| ||| | || || ||||||||  | ||| | || || ||||||||||| |||||||| ||||| |||||||| || ||||||||||||||||||    | || ||  |  |  |  |  |     ||| || ||||   |  | |     |||   ||   | | || |    
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgta----agtccct--cgaatcaccttgacgctctcacttgttctctgatctgatcatcttatcattgctttcttgcag---

upper sequence: GLYMA06G04390.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ32930 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgta------ttata---ttcacttacacactatatc--tagttcttcag---ttattcttataattaacatggttaattttaaat-gcatgaattag------------------------------------------------------------
 |||||||| ||||| || || || ||||| |  ||  |  | || || |||||||| ||||| |||||||| || ||||| || |||||||||||||| ||         |||   ||   || |||||    ||  ||||||||  |   | | ||   || ||  | | |  | || |  ||  | || | ||                                                             
GTTCGTCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcccatacgttttctttccacacctcctccatagttctttggagttcagtcccttagtt--cttcgccagttgtcgatcacttgcagtactcagcttcagcattttgtcaatgatgttgcgcactgaacttcgttcttgtcgactcgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGTCGTTTGGCGTCCTCCTGAGTTCGCAAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCAAGCTTCGTTCGCCAGCTCAACACCTATgtattatattcacttacacactatatctagttcttcagttattcttataattaacatggttaattttaaatgcatgaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA