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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacggatgtcacag

Basic information

species Arabidopsis thaliana
transcript AT4G23100.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 4
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacgg--atgtcacag--------------------------------------------------------------------
|||||||||||| |||||||| |||||||| || ||||||||||| |||||||| || || ||||||||||||||||| ||||||||||||||||| ||||||||    |    |    |     |   |||  |  ||     |    | | |  |  | |  |  |  ||| || |                                                                     
AAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgcgcactgcatccctgtattaacttcttgctttatgtgattttcagttatgatttgtgcattgccatgccatatatatcttcagtccgaaagtttttttttttgccagcagttgatccaatccgaaacgtctattcttgtag

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacgg--atgtcacag----------------------------------------------------------------
|||||||||||| |||||||| |||||||| || ||||||||||| |||||||| || || ||||||||||||||||| ||||||||||||||||| |||||||| |  |    |    |     |   |||  |  ||     |    | | |  |  |    |  |  ||| || |                                                                 
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataat-tattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacggatgtcacag---------------------------
|||||| ||||| |||||||| || || || || |||||||| || ||||| || || || ||||||||||||||||| |||||||| |||||||||||||||| |||    | | |  ||| |   | |   || | || |  |  || |  | |  |   | |  |  ||| ||                             
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATCTTTATCAGgtaacttctcttacattgcattccttgtacag-catcttaca--gaaactatgatctta--gtttgtgtgtgttaccattcttttgtcagagataatacagtacc

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttc-------aaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacggatgtcacag----------------
|||||| ||||| |||||||| || || || || |||||||| || ||||| || || || ||||||||||||||||| ||||| |||||||| |||||||||| |||        | | |   | || ||  |||      |  |||   |||        |   | | |    |  | |||                 
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATCTATATCAGgtaacttctctttctgacgttttcttttccctgtgcatcttgcagaaattatgatcttagctcgtgtgtgtttttacttgacattatataagactgacca

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 4
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgta---atttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacggatgtcacag----------------------
 ||||| ||| | || ||||| |||||||| || |||||||| || |||||||| || |||||||| |||||||||||||| ||||| || ||||||||||||    ||||   |||   ||   ||| |  |       |   |   ||   ||    || | | ||||    ||| |                       
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACCTTTATCAGgtacttgtttcgctgatgcataa-accattttttcttttttgccattggagtgatttgaaattttttacgcg-atcatattttctacagatgaatatgtata

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 4
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataat-tattgccaatgctctcaccctaaaacgtgac---aaataaccaactatctacggatgtcacag--------------------
 ||||| ||| | || ||||| |||||||| || |||||||| || |||||||| || |||||||| |||||||||||||| ||||  || |||||||||||| ||     | | ||  |||  |  |  | |  || | | | ||||     |||    |   |   |    |   || |                    
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACCTTTATCAGgtacttgtttcgctgatacattaactttttttttgccattaga-gtgatttggaatttttatgcaatcatattttctacggataaatatgtatcatcattg

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatc-tacggat-gtcacag---------------------
|||||| ||||| ||||| || |||||||| |||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||| |||||||||||| ||   |   |  |  ||    ||  |||      |  ||  || |   ||   |   || ||  |||  | | |                      
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag

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|124714716|gb|EH806118.1|EH806118
EST:     TTCACATCTTTATCAG                         GTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
genomic: TTCACATCTTTATCAGgtaatttcaa ... gatgtcacagGTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
EST: gi|116484545|gb|EG527137.1|EG527137
EST:     TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAG                         GTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
genomic: TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaa ... gatgtcacagGTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
EST: gi|47831536|gb|CK121220.1|CK121220
EST:     TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAG                         GTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATCGGCTTC
genomic: TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaa ... gatgtcacagGTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
EST: gi|47830326|gb|CK120010.1|CK120010
EST:     TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAG                         GTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
genomic: TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaa ... gatgtcacagGTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
EST: gi|116484547|gb|EG527139.1|EG527139
EST:     TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAG                         GTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC
genomic: TTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaa ... gatgtcacagGTAAAAGCAGTTGCTGAGGAAATGGGAATTGGTTTCTTAGGAATTGGCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacggatgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG