Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag

Basic information

species Glycine max
transcript GLYMA20G35090.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttc----ttgttcttgcgtctt--gattcttttacttgtttttgtttcattcctctgcagtatagca------agtggtaactgtcctacgtttgcag-------------------------------------------
 || ||||||||||| ||||| ||||||||||||||||| ||||| |||||||| ||||| || ||||| || |||||  | ||||||||||||||||||||      |||  |    || ||  ||| | ||  |  | |||       |    | |||      ||  | || |||      | ||  || | ||||  |||   |                                            
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaat-tcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag

upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag
 || || |||||||| ||||| || |||||||||||||| |||||||||||||| |||   || ||||| || |||||  | ||||||||||||||||||||   |  |  | | | ||       | |  |   |   |||| |     ||      ||| |||                                
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatattttcctttctacag--------------------------------

upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtt--tttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag--------------------------
 ||||| ||||||||  | |||||||||||||||||||| || |||||||| || ||||| |||||  | ||||| ||    |||||||| ||||| |  ||     ||||       ||||     ||| ||  || |||  |    |   |   |  | |     | |  |   | || | |||      ||  | |                          
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag-----------------------
 ||||| ||||||||  | |||||||||||||| ||||| || |||||||| || ||||||||| |  | ||||| || |  || ||||| || |||| |||     |||| | |||    |  ||     ||| ||  |||  ||  ||| | ||  | | || |  |      ||||  |  | |  || |   |                       
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGTATGGCTCAGGAGCCTGTTCTTTTTGAAGATGTTGTTTGTCAAATGGCTGACATGATAGGGCCAGCGgtaagcatttgcttttgaagatttgtacaagttcattctcttccttgagttgctttagtgttcaatgaattggtcggtacttagcatgggtgtattgttgacatctacccttcactgcag

upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttg----cgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacg--tttgcag------------------------------------
 ||||||||||||||  | |||||||||||||||||||| || |||||||| || ||||| |||||  | ||||| || |  || ||||| ||||| | |||  |  |||| | |    |||           |||  | | |   |  ||| |  |  ||      |  |   |  | |  ||||      |   |||| |                                     
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag

upper sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ32791 (Selaginella moellendorffii), 5'ss of exon 10
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag
||||||||||||||| |||||||| ||||||||| | || ||||| || || || || || || ||| | || |||||   ||| |||||  | ||||||||     || | | ||  | | || ||  |  |||  |   || || |||     ||   |||||                                
CTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAAGACCCCGTCCTCTTCGAGGACATAGTCTGCCAGATGACGGACATGATCTGCCCAGAGgtgcg--ttagctgtt--tgtagcttccgggctctcgtcaatgcttatgt---gatcgattgcag--------------------------------

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|8403556|gb|BE059190.1|BE059190
EST:     TGCTGTATGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAT                         AATGAGGGATATATCACATTACGAGATGT-AAAGGCA
genomic: TGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttcttt ... acgtttgcagAATGAGGGATATATCACATTACGAGATGTTAAAGGCA
EST: gi|51343535|gb|CO984268.1|CO984268
EST:     TGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAG                         AATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA
genomic: TGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttcttt ... acgtttgcagAATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA
EST: gi|8403723|gb|BE059419.1|BE059419
EST:     TGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAG                         AATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA
genomic: TGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttcttt ... acgtttgcagAATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA
EST: gi|21887061|gb|BQ740274.1|BQ740274
EST:     GATTGGACCAGAG                         AATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA
genomic: GATTGGACCAGAGgtttttcttt ... acgtttgcagAATGAGGGATATATCACATTACGAGATGTTAAAGGCAGTAAACTTTCTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA