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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcattgcacacgaataattcttctttaaatgatctccaactcgcataacacgttctcatacttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

Basic information

species Arabidopsis thaliana
transcript AT4G24190.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
-------------------------gtttgcattgcacacgaataattcttctttaaatgatctccaactcgcataacacgttctcatacttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                          |||        | | ||||    | || |  ||   ||  | ||    ||| || ||      ||| |||| | |||| |||| |||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| ||||||||||| || |||||||| || || ||  
gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatc-cctggagcttaactaatacttttgttatcttttgttgc-agGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
---------------gtttgcat-tgcacacgaataattcttctttaaa--tgatctccaactcgca-----taacacgttctcata-----cttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
               | | |  | | |||    || ||  |   | | |  ||   | || || |       |||| |  || | |       |||| |   ||||||||||||||||| ||||| || || || ||| ||||||| ||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||||||| 
gtattttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 15
---------------------------gtttgcattgca-cacgaat-----aattcttctttaaatg-atctccaactcgcataacacgttctcat---acttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                             || |||| ||    |        ||| |  ||| | | | | |  |    ||| |     ||| |  |     |||| ||  ||||||||||||||||| |||||  | || || ||| ||||||| ||||||||||| ||||| ||||  ||||||||||| ||||||||||| || |||||| 
gtatatatgtatgctgctggtttatccactttcattacagtgtggggtctggaatacagcttgagaagtaccaacgctgcgcttgttttgttttgttttgttttgtttttgcagGTCATCTTCTTCACCGACCCTATGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAGGAAGTTCCAGAACGTGTCCAAGGAGGGCCTGAAGC

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
----------------------------------------------gtttgcattgcacacgaataattcttcttta---------aatgatctccaactcgcataacacgttctcatacttgtgttcc-cagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                                              |||  |     |||  |    ||||  | |           ||||| |        |  | |   || || |     | | |  ||||| || |||||||| || |||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| ||  ||||  
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------------gtttgcattgcacacgaata---attcttctttaa----atgatctccaactcgcataacacgttctcatacttgtgttcc-cagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                                                        |||  |   ||   |  |    ||||| ||   |    ||||| |        |  ||    || || |     | | |  ||||| || |||||||| || ||||||||||| |||||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| ||  ||||  
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------gtttgcattgcacacgaataattcttctttaaatg----atctccaactcgca-taacacgttctcatacttg--tgttcc----cagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                                        |  |||   |  |  | |||||| |   || |    |||      |   |  |||  ||| || | ||      |||     ||||| || ||||| || |||||||| ||||| ||| ||||||||||||||||||| || ||||||||||| |||||||||||||| |||||||| |||||  
gtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATGGACTATGAAGACAAAAAATTCCAGAATGTGTCAAAGGAAGGCCTGAAAC

upper sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------------------gtttgcattgcacacgaat--aattctt----ctttaaatgatctccaactcgcataacacgttct---catacttgtgt-tcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                                 |||| |     | | |    || | ||     |||     ||   ||     |  ||||| |  |    ||  ||| |  |  ||||||||||  || ||||||||||||||||| |||||||  ||| ||||||  || || || |||||||||||||| ||||  |||||||| |  || ||| 
gtaaagcgctgtatctgattgtttatagtagtttttggaacatgctcaagctcaacttttatggttttggcgcatagtcagacatctcaacacttaatgaatatgattgcgggtttcagGTCATCTATTTGACAGACCCAGTTGATGAGTACTTGACCCAAAACCTGACTGAGTATGAGGACAAAAAGTTCCAAAATGCTTCCAAGGACGATCTCAAGC

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|124915909|gb|EH989783.1|EH989783
EST:     AGCTAGAGAAATCTCCATTCCTAGAGAGGCTCATCAAGAAGGGCTATGAG                         GTCATCTTCTTCACAGACCCAGTTGATGAAT
genomic: AGCTAGAGAAATCTCCATTCCTGGAGAGGCTCATCAAGAAGGGCTATGAGgtttgcattg ... gtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctttaaatgatctccaactcgcataacacgttctcatacttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG
                        gcataac  putative branch site (score: 3)
                                              tgttccc  putative PPT
     tttaaatgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcattgcacacgaataattcttctttaaatgatctccaactcgcataacacgttctcatacttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG