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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagtaccttgtgaccttttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC

Basic information

species Arabidopsis thaliana
transcript AT5G19820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 2
-------------------gtaagatcccctgtt---tctctgtgaatataatcttctaacactttctaaagcagtaccttgtga---ccttttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
                    || |||      ||       ||  | |  |||    |||  |||||||  | | |   ||   |     | |  |   |||| ||||||||||||||||| ||||||||||| || || || || ||||| || ||  | || || || || ||| |||| |||||  ||||||| || |
cttttattctttgtagtcattatgatttatgattgaagtcatgctatttaaattaaataa-gctttctattgtaattattttcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGAATAGTTAGCAAACTACTTGTACTTC

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
----------------------gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagta--ccttgtgaccttttc-atgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
                       | | |      ||     ||  | | ||||    |||  || |||   | | |    ||    |  || || |   |||| ||||||||||||||||| ||||||||||| || || || || ||||| || ||  | || || || || ||  |||| |||||  ||||||| || |
ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataa-gctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC

upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagtacc-ttgtgacctt--ttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
                      |   ||      |||    ||   |    |    | | | ||  ||| |   | || ||||        ||  |  |||| |||||||||||||| || |||||||||||||| || || ||||| || || ||  | || |||||||| ||| | ||  |||| ||||| || || |
agtggctcagtgctcaagattattttatttttaattttctcgttctttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatataatcttctaacactttctaaagcagtaccttgtgaccttttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
                                          ccttttcat  CT-rich tract
     ataatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagtaccttgtgaccttttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG