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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os08g36700.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA04G04200.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccatt-acgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag-----
||||||||| ||||| || || || |||||||| ||| | || || ||||||||||| |||| ||||||||||  |||||| ||||| |||||||| ||||||    ||| || | |    | ||    | || | | |  |  ||   |        | |    | |  |   |||  || |     |          
CTTCGTCGTTTGGCGTCCTCCTGAATTCGCCAGAGACCTTCTTCCTAACTACTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtattatatttacttacacactgatacactatctctagttcttcaattattgttttcttttctttttat-attctgacagttttaaatggatgaactag

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G35980.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccat-tacgttcgtgat-catggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgat-ggtgtgtcgcgtgcag------
||||||||| ||| | || || || ||||| |||||| | ||||||||||| ||||| |||| ||||||||||  |||||| ||||| |||||||| |||||| |     |||   | | ||   |  | |||     || ||     ||   | | | |   ||  ||| | | |  |   |   |   |           
CTTCGTCGTTTGGAGACCCCCCGAATTCGCTAGGGACCTTCTCCCCAACTATTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtatgtatcatacacccatcatgtctctcttctttttcttaatttctactcatacgttcttccga--gacaatcttattcaatacattatgaaacactaaat

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA14G09190.1 (Glycine max), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccat-tacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggt-gtgtcgcgtgcag------
||||||||| ||| | || || |||||||| |||||| | ||||||||||| ||||| |||| ||||||||||  |||||| ||||| |||||||| |||||| |      ||   | | || ||  |   ||    ||  |      ||     ||   |  |  || | |  | ||| | |   |     ||       
CTTCGTCGTTTGGAGACCCCCCGAGTTCGCTAGGGACCTTCTCCCCAACTATTTCAAACACAACAACTTCTCCAGCTTCGTTCGCCAACTCAACACCTATgtatgtatcacacacccatcat-atctctcttctttttttcttttttttttttaagttcttttatcgaaggcaatcatgtttgaaacattatcaatcaata

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv18s0001g10380.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtga------tcatggcgtctcgccattgatggaagcttgaagggt-----------gtatggaatgacgaccgtgatggtgtgtcgcgtgcag---------------------------------
|||||| |||||||| || || ||||||||  | ||  |||| ||||| |||||||| |||| |||||||||   ||||||| | ||||||||||| |||||| ||| |  |  || |        ||    | ||    | ||  ||||    | |  |||            |||| ||  |    | |  || | |  |   |  ||                                 
CTTCGTGGTGTGGCGTCCTCCTGAGTTCGCTCGCGATCTCCTTCCCAATTACTTCAAACACAACAACTTCTCAAGCTTCGTCAGACAGCTCAACACCTATgtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactag

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ15796 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccat---tacgttcgtgatc-atggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag---------------------------------------
 ||| |||| ||||| || ||||| ||||||| ||| ||| | || || |||||||||||||  |||||||||   |||||||| ||||||||||| || ||  | |     ||||||     || |   |  |||    ||  | | || |       |   |          | ||  |    |   ||   ||                                        
GTTCATCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcgcatacgttttctttccacacctcctcatagttctttggagttcagtcccttagttcttcacttgcagtactcagcttcagctgtcaatgatgttgcccactgaacttcgttcttgtcgactcgcag

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ31857 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacg--ccattac------------gttcgt--gatca---tggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag-------------------------------
 ||||||||||||  ||| || ||||||||||  ||  | ||||||| |||||||||||||| |||||||||   ||||||||| |||||||||||||||||  |  ||||| |            ||||||  | ||    || | ||    | ||        |||  |  | |  |    |     || ||   | || || |  |||                                
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgtttgcttcgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ28850 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag
||||||||||||| |||| || ||||||||| | ||| | ||||| |||||||||||||||| ||| ||||||  |||||| || ||||||||||| |||||  | |  |    ||    | | |   || |    ||    ||    |||      ||| |  |  ||  | ||  |               
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtgagtctctcgaatcaccttgaagctctcac-ttgttctccga--tctgatcatcttatcg--tcgcgttcttgcag---------------

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ38003 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacg--ccattac--gttcgtgatcat--ggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag----------------------------------------------
 ||||||||||||  ||| || ||||||||||  ||  | ||||||| |||||||||||||| |||||||||   ||||||||| |||||||||||||||||  |  ||||| |  | || || |  |  |    |||||  |   |       |       || |       ||| |||  || | ||   | ||||                                               
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagttccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgt-tcttccaccgagcgttttgctttgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ17520 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag
||||||||||||| |||| || ||||||||| | ||| | ||||| |||||||||||||||| ||| ||||||  |||||| || ||||||||||| |||||| | |  |    ||   | | || || ||| |  ||| |    | |   |   | | |   ||  |   | ||  |               
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtaagtccctcgaatc---accttgacg-ctctcacttgttctctgatctgatcatct-tatcattgctttcttgcag---------------

upper sequence: LOC_Os08g36700.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ32930 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggt-gtatggaatgacgaccgtgatggtgtgtcgcgtgcag---------------------------------------------------------------
 |||||||| ||||| || ||||| ||||||| ||| ||| | || || |||||||||||||  |||||||||   |||||||| ||||||||||| || ||  | | |  | | |||  || |  |    | || |  || |    ||| ||    ||     |   |  |     | ||   || | |||||                                                               
GTTCGTCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtc-tcccatacgttttctttccacacctcc-tccatagttctttggagttcagtcccttagttcttcgccagttgtcgatcacttgcagtactcagcttcagcattttgtcaatgatgttgcgcactgaacttcgttcttgtcgactcgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGTCGTGTGGCGGCCACCGGAGTTCGCCAGGGACATCCTCCCCAACTACTTCAAGCACAGCAACTTCTCCTCCTTCGTCCGCCAGCTCAACACATATgtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA