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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA

Basic information

species Arabidopsis thaliana
transcript AT2G32000.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os09g32450.1 (Oryza sativa), 3'ss of exon 11
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
                                  | ||  ||||      |  || || || || |  |  ||  ||||  |||    | |     |||   | | | |  |      |  |||| | |||  | ||||| |||||||||| |||||||||  |||| ||||||||||||||| |||||||||| ||||||||||||||  |||| ||| |||
---------------------------------gtatggcttgtgaatttattcacatcac-atgagctcacctttttt--ttttgggtctgaaaatgttcataattatcattcttcattaagGGTAGCACCACACCTCCTGACTACCTTAGTGAGAGTGAATTGATCTCTCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTGCATGTAA

upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G102181_T01 (Zea mays), 3'ss of exon 6
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
                                  |  | | | |       | ||||  ||    |||     |  |||  |     | |  ||||  |   | |   || |      |  |||| | |||| | || || || ||||| ||||| |||||  |||| || |||||||||||| |||||||||| ||||||||||||||  ||||||||||||
---------------------------------gtaaggtctatcagtttgctcaaaccac----atgcacttaacttttatcaggatatgatgttgatcaatcataattctttg--ttgaagGGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAATTGATTTCCCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTACATATAA

upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G36800.1 (Glycine max), 3'ss of exon 11
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
                       |   |     | || ||  | |  || | | |  ||   ||    || ||| |     | | | | |  |     ||  | ||      ||| ||| ||||||| |||    ||||| || | ||||||||| |||||||||||||| || ||||||||| |||| ||||| ||||||||||| ||  |||| ||||| |
----------------------atacatataaccatttctggggagaagaaaaaaggttgaaattcatttcccattggagttctgtgtgtattacacatagct-aacaccacaaattctgcagGGGAGCACCAGTCCTCCAGATTTCCTTACTGAAAGTGAGCTGATATCCCTGATGGAGAAGAATGGAATAGGAACAGATGCATCGATTCCTGTTCATATTA

upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0062g00860.t01 (Vitis vinifera), 3'ss of exon 9
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattacta-taatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
                               ||          ||||| ||   |||     | |  ||      ||  || | | | |  |   |   ||||      || | |||| || ||||| | ||    ||||| || || |||| ||| |||||||||||||| || ||||||||| |||| ||||||||||||||||| ||  |||| ||||| |
------------------------ggaaagactagagatcaaatactatgatgtaaaacctgagtgttgaacatgctactaatatttctcataactacttattaactgtttatgaaatttatagGGGGAAACCAGTCCTCCAGATTATCTTAGTGAAAGTGAGCTGATATCCCTAATGGAGAAGAATGGGATAGGCACAGATGCATCCATTCCTGTGCATATTA

upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S474_3V6.1 (Physcomitrella patens), 3'ss of exon 11
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
            |  |       | | || ||| | |||  || |    | |  ||||  ||        ||| | |  ||  |   |||  ||   | ||| |  | ||     || | ||||||   ||| |  |||| || ||  | ||||| ||||| || ||| |||| ||||| ||||||||||||||||| ||||| || ||  | || || || |
-----------ttgtatgcaccataaatgttct-tctgccctgcat---gtcttaaatacctg------gtcctcatgcagcattggtttgttgaaagcattggtctattt--ggatgtgcagGGGCGAACTTCAGCTCCAGATTATTTAACTGAAAGTGAACTCATAACTCTAATGGAAAAGCATGGCATAGGCACTGATGCGTCCATTTCAGTGCACATCA

upper sequence: AT2G32000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ20813 (Selaginella moellendorffii), 3'ss of exon 11
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
                                                             ||||   | || |   ||     ||| ||| | ||    | |   | ||||        ||||| |  ||  | ||||| || ||| | |||||||| || ||||||||||| |||||||||||||| || || || || || || ||  | || ||||| |
------------------------------------------------------------gtataccatctcaaagcttttcccattgttt-tattctcgtcttggtcttgt--------cagGGAAGAACCTCTCCTCCTGATTACTTGACTGAGAGCGACCTGATATCTCTGATGGAGAAGCATGGGATTGGTACGGACGCGTCCATTCCAGTGCATATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA
       ttttagtttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacattcttctccagtttttgttactgctctctttgctttgtactaggacacaaattactataatgtttccacttttagtttattttttctgtttgtatttgaatgttgtaaaatctacagGGGAACACTGCGCCTCCGGACTACCTTACTGAGAGTGAGCTGATATCTCTCATGGAGAAGCATGGCATAGGCACAGATGCATCAATAGCTGTACATATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG