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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG

Basic information

species Arabidopsis thaliana
transcript AT2G28310.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 10
--------gtaagtctctctttgaaacgttctctttagagcaactcaaga------gtgtttagtcattgtca----gtactgagttttctgaaaaaaatt-ccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
         ||  ||||| |    |   || |||  ||  || | ||| |      | ||  |     | ||     |   |  | |  || |   | ||| |  |    ||| ||||||||||||||||| || || || ||| |||| |||||| ||||||| |||||||||||||||
gtatgtgattatttctctgtcctgagttttgtctacagtacatcccaatatgtatggcgtgaaagtgctatccacttgagttaggctaactaatctatattgctgttgttcagCTTTGTTGAAATAATGGCTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
           | || | | | ||| |     | |||   | ||   |  |   ||| |  |  | |  |    |      ||   | | |||| ||||||||||||||||| || || || ||  |||| |||||| ||||||| |||||||||||||||
----------gtatgtagcttcctcct-----ctactt--gggtagctgatgtatgtgaaga--ggggctaactatttgtgtttgatgt-acagCTTTGTTGAAATAATGGCCCCGGTGTTCTCCAGAGATGCATGGAGATGTGTATGGCATATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 9
-------gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
       | ||      |   |  |            || |     ||| |||||  |  || | |  |||     |  | | |     |  | |   ||| ||||||||||| |||||  |||| || ||| | || |||||||| ||||| |||||||||||||||
acatgaaggaaaaacagcaacggcataacaaaacggaaggaggatcaga-tgttttctttttcttaaaactatccgtcttcacattctgtttcacatgcagATTTGTTGAAATTATGGCAACTGTGTTCTCTAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgttta----gtcattgtcagt--actgagttttctgaaaaaaatt-------ccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
||| || | | |||       ||     ||| || || |  |||    |       |   |||||   |      | | ||   || ||       | || | |||| ||||||||||||||||| || || || ||  |||| |||||| |||||||||||||||||||||||
gtatgtgtttttttt---tcctcctcccagaaca-cttaccagttcccataatactaccatcagtctcccatacatacagaggcaacttatgtatgctctattacagTTTTGTTGAAATAATGGCTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 10
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
            | | |  |   || ||           ||| | |||  | || |  | | |||   ||| | | |   | ||       ||||||||||||||| |||||  ||||||| ||  | || |||||||| ||||| |||||||||||||||
-----------gtaggagtgcaatcattta-------ttagattattttcttatcgaaatttctg---tttttcacatgtaatctgatatgcagGTTTGTTGAAATTATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
------------------gtaagtctctctttgaaacgttctctt--tagagcaact--caagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcac---agGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
                      ||      |||||  | | | ||  || | ||  |  | ||| | | |  || |||||  |||| ||||  ||  |  | ||    | | |    || ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||| |||||||||
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtc--tacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 10
--------------------gtaagtctctctttgaaacgttctcttt--agagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctca---cagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
                        ||      |||||  | | | ||   | | ||  |    ||  |||  |   | ||  |||| ||||  ||  |  | ||    | | |    || ||||| ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||||
gtatgctctctctcttccaccctggttcaaagttgaattgatgtattgcaatatcatttacctagattttcttttctttctctacttagttaactttactatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAGGCTTGGCGTTGTGTGTGGCACATGATTCAG

upper sequence: AT2G28310.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------------------------------------------------------gtaagtctctct-ttgaaacgttctc--tttagagcaactcaagagtgtttagtc----attgtcagtactgagttttctgaaa---aaaattccctct-----cacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
                                                                                       ||||   |   | || |||  ||       ||| | || |     || ||  | |    ||| ||    ||      ||| |     | | ||  ||         ||| ||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||||||||||||||||||
gtatgctttctctctgttctccctctcttgcatatctggtgtgcgtgaatttgtctttatgagtgttaaaacatgcataaacacaatgtaaaaataaatattcaaatatttgtaacatagggtaaatatgttgtcttgggacttgcattttctcccctctcccctcttaggcttacagttttctacattaattcagATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG
                                          ttccctctcac  CT-rich tract
                            ttttctgaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctctttgaaacgttctctttagagcaactcaagagtgtttagtcattgtcagtactgagttttctgaaaaaaattccctctcacagGTTTGTTGAAATAATGGCGCCTGTATTTTCTCGAGAAGCATGGCGATGTGTGTGGCATATGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC