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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc...

Basic information

species Zea mays
transcript GRMZM2G054136_T06
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
|| |||||||||||||||||||| || ||||||||||| || ||||| |||||||| |||||  | ||| |||| ||||| || ||||| || || ||||||| | || ||   | | ||   |  ||| || |    || ||      ||    |  ||||| |||   || | | || | | |               
GGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTCTTCACAGGGgtaaaaaggctctatttctattattgactttcgg----atattca----tgcccttgctctgaccatattatgttacttgtatggcag------------

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagag-acttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
|| ||||||||||| || |  || || |||||||| ||||| ||||| ||||| || |||||  | ||| ||||||||||||| ||| |||| || ||||||||   | |  |   ||      | |  | |     | || | ||   || | |  | |       ||  || | |||  | |     |       ||  
GGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGCTTCACAGGGgtatgatgtagctttgatgcttttttttttgttcaacctatatgttcggcttagttctgtgccctttttatattttaatctttttaaatcaaatccattt-

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 5
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttt-tactctgattctta-tctgaacattcgatatcaattctgtagggactccctgcttcc
|||||||||||||| || |  || || || ||||||||||| || ||||||||||||||||| |||||  ||||||||||||| ||  |||| ||||| |||||    | |||  |       |||| | |    |  ||   |  |  || ||| ||| | ||||   |  ||   | |   ||      |   ||  |  
GGTTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGCTGCATAGAGgtatgtcta-ttctgaagccttttgtattttgctgattataaatacatcctaattattagtttgaagcattcattcaactcacgtgttctatatttgaatt-

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G09330.1 (Glycine max), 5'ss of exon 2
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtata--------gagacttcctatttacagtgtactctcagc-accatcttttactctgattcttatctg-aacattcgatatcaattctgtagggactccctgcttcc
|| ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  |||||| |||| ||||||| || |||| |        ||  ||||   |||  | | |    |||   | ||| || || | || |  | ||||| | |||| |   ||||  || |      |   ||| |  
GGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGCTCCACAGAGgtagaactgtaatgaagcttcaattttttaatttgtgatcatttaacatattataatgtg-tcatcatctgcagcatttgt--tcaaccctct-----ttttgtgcat--

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G31840.3 (Glycine max), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc--
|| ||||| ||||| ||||  ||||| |||||||| ||||| ||||| |||||||| |||||  ||||  ||||||||||||| ||| |||||||||| ||||   |   |       | || | || | |        | | | | |  ||||  | |  | |   | |||   | | |  |          ||  | |  
GGATATGTTTTCAAAATCACCGGTGGGTGTGACAAACAAGGATTCCCTATGAAGCAGGGAGTGCTGACCCCTGGTCGTGTTCGACTTTTGCTCCATAGAGgtaggaatgttctactgcttcaatctattgttgttttggtttataatt--gattgatgttggcagcattgatccaactgccatgttctgcatttggctgcgg

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G24630.1 (Glycine max), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatc-tgaacattcgatatcaattctgtagggactccctgcttcc
|| ||||| ||||| ||||  ||||| |||||||| ||||| |||||||||||||| ||||| |||||  ||||||||||||| ||  |||||||||| ||||       ||        || |||| | |        | | | | | | ||  ||||  |  |     | |        ||     ||| ||   ||| 
GGATATGTTTTCAAAATCACTGGTGGGTGTGACAAACAAGGATTCCCAATGAAGCAGGGAGTGTTGACCCCTGGTCGTGTTCGACTCTTGCTCCATAGAGgtaggattgttttactgcctcaatgtattgttgttttggtttataaatatcataattataattgattgctgttgatggcattgatacaactgccgtgttc-

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G08210.1 (Glycine max), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttt-tactctgattctta-tctgaacattcgatatcaattctgtagggactccctgcttcc
|| ||||||||||| || |  || || || ||||||||||| || ||||||||||||||||| |||||  ||||||||||||| ||  |||| ||||| ||| |    | |||  |       |||  |||    |  ||   |  |   | ||| ||| | ||||   |  ||   | |  |||      |   ||     
GGCTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGCTGCATAGAGgtttgtcta-ttctgaagccttttgttttctgttgattataaatacatcataattattagtttgaagcattcattcaactcatgtgttttatatttggaat-

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G45770.1 (Glycine max), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagag-acttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc-
|| ||||||||||| || |  || || |||||||| ||||| || ||||||||||| |||||  ||||| ||||||||||| | ||| |||| || ||||||||   | |  |   ||   |  | |  |     |   || || | ||  | |   |  |   |  ||  |  |   || |  |   | ||| |  ||   
GGCTATGTCTTCAAAATTACCGGAGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTGACTCCTGGTCGTGTTAGACTTTTGCTTCACAGGGgtatgatgtagctttaatgccctattttgttcttcctatattttctgcttagttctgtgcccttatgttttaattt--ttttaaatcaattccatttttgtg

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctat-ttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc--------------
|| || || |||||||||| |||||| || || |||||||| |||||||||||||| |||||||||||| | || |||||||| ||| |||| ||  | ||||   | || |  ||  ||    |  ||| |      ||||| | |    ||||  ||| ||    |  |       | ||||||     |  || |||               
GGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGCTTCACCGAGgtaactaaacataataccttttcttacacttttg----catctataatg--gatttgtatttgtgtgtgtgtgtgttttgctgtagattaacattgtttcgtaatgggtgaacag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgta-tagagact-tcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
|| || || |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||| | ||| | || ||||| |||||| |||| ||  | |||| ||||  |   || ||| | |   |     ||||  |   ||||    | | |||| | ||    ||   |||  ||    |  ||      || ||  
GGATACGTATTCAAGATCATGGGAGGATGTGACAAGCAAGGTTTCCCAATGAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagattccaccccattgataaaat-tatacagcttctctttttttcattaatcttctgtg----ttttttatttatgtgatctggttattgtgtttag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagact-----tcctatttacagtgtactctcagcaccatcttttactctg-attcttatctgaacattcgatatcaattctgtagggactccctgcttcc--------
|| ||||| ||||||||||||||||| |||||||||||||| || || |||||||| |||||  ||||| |||| |||||| ||||| |||| |||||||||    | |||     |  | |   |  |  |  || | ||| | | || | |    ||| ||||   |        ||| |  | | |    |||   |||||          
GGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGCTTCATAGGGgtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagttgggtctatgagatttattac-actttatgcttatttgagcag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagact----tcctatttacagtgtactctca-gcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc------------------------------------------------------------------------------
|||||||| ||||| || ||||| || |||||||||||||| || ||||||||||| |||||  ||||  | || || || |  |||||||| || || |||    |||||    | ||| ||   |  || |   | |    |   || | |    || |||| |     || |   |  |||  |         |||| |  |                                                                              
GGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGCTTCACAGAGgttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 5'ss of exon 4
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgta------tagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatc-tgaacattcgatatca-attctgtagggact---ccctgcttcc----------------------------------------------
|| ||||| ||||| |||||||| || |||||||||||||| |||||||||||||| ||||| || ||| ||||||||||| ||||  |||||||||| |||       | | |   |  || |    ||| |||  |  |     |||  | | | |     |||  |  || |    | ||  || ||   ||||       || | ||                                              
GGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGCTCCATAGAGgtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagcatgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttttgcttaagcag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: PP1S253_38V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattct--tatctgaacattcgatatcaattctgtaggg-actccctgcttcc-----------------------------------------------------------------------------------
|| |||||||||||||||||||| || || |||||||| || |||||||||||||| |||||| | |||   || ||||| |  || ||| | || || ||||| | ||             ||||             |    || |||||       || |      ||| |     |  |||     |  |  ||  |                                                                                     
GGGTATGTCTTCAAGATCATGGGAGGCTGCGACAAGCAGGGTTTCCCAATGAAGCAGGGAGTTCTCACTCAAGGCCGTGTGCAGCTCCTGATGCACAGAGgtatggcgatagatagacacgggtgttggtgtcatgaagtaggctagtctgaacgagacatttatgtcctcgctgctcctcttgtgcaacaagcgttgagtggggttgtggagtggtttgatgggctcagtatgggtgcgagaatttagttctcccttttgtaacgattattgtgtgttgttgcag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcc-tatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgat-atcaattctgtagggactccctgcttcc------------------------------------------------------------
|| |||||||||||||| ||||| || || |||||||| || ||||| |||||||| |||||| | ||    || ||||| |  ||  || | || || ||||| || |    |  |  |    |||      || | ||| | |  |     | | |  |||  ||       || | ||  || |     || |   | |                                                            
GGGTATGTCTTCAAGATTATGGGAGGTTGCGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTTCTCACACAAGGCCGTGTGCAGCTCTTGATGCACAGAGgtatggatataaacacagctggtatgtctgagtag-atcatttatcgcgtcactgcctcgctgtgcagaaagcgatgagttgcgttgaagtacctttgatgcactcagtacggccgcgaggttatgattttcatctgtaacgactcttgcctgttgtcgcag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: PP1S311_33V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattc-ttatctgaacattcgatatcaattctgtagggactccctgcttcc--------------------------------------------------------------------
|| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || |||||    || ||||| |  || ||| | ||  | |||| | |   |  | |  | | |  | ||||   ||    ||  | ||  || |  || ||     ||   | |  |  ||  || | || || | ||| |                                                                    
GGATACGTTTTCAAGATTATGGGAGGATGTGACAAGCAGGGTTTCCCCATGAAGCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAGgtaca-acgttaaccacctgccgcttcctcttgtcatg--ctagtgctgggaataattgtcgatggatgtaacagaacgtcactatgcacacc-tacttacaaggcgcgtcttgattttcggttgcaactataatgcagtaaagtaatgaaatttttgttcttctgaag

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: PP1S311_33V6.2 (Physcomitrella patens), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTT-TTGACTTCTGGTCGTGTTCGTCTTCTGC-TCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
                || |   |   | ||||||||  | ||| |  | || |  ||  ||      |||   |  | ||||      | | |    | |  ||| |     |   |    ||| ||   | ||  |                                                                
----------------TCGTCAATTT-TATGACAAGC--GTCTTGCTCAAGAGgtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaag--------------------------------------------------------------

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
|| |||||||||||||||||||| |||||||||||| | |||||||| |||||||| || ||  | |   |    ||||| || || ||| |  |  | |||| |  ||       |||         |||   | || |||||   |||||||         | |||||  | ||                        
GGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgatgcttctttt--------ttcttttctccctctttcgttctgattt-------gagattcgtgaccag-----------------------

upper sequence: GRMZM2G054136_T06 (Zea mays), 5'ss of exon 3
lower sequence: EFJ26393 (Selaginella moellendorffii), 5'ss of exon 3
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc
|| |||||||||||||||||||| |||||||||||| | |||||||| |||||||| || ||| | |   |    ||||| || || ||| |  |  | |||| |  ||       |||         |||   | || |||||   |||||||         | |||||  | ||                        
GGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgatgcttctttt--------ttcttttctccctctttcgttctgattt-------gagattcgtgaccag-----------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29577181|gb|CB617293.1|CB617293
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|31664073|gb|CD573253.1|CD573253
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|22521636|gb|BU080447.1|BU080447
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|148942260|gb|EC887276.2|EC887276
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|149075315|gb|EE163821.2|EE163821
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|32845854|gb|CD985535.1|CD985535
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|16137351|gb|BI894216.1|BI894216
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGAG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 867

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 838

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 787

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagggactccctgcttcc

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG