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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacataacaatttacattgtctagttttcagttggtttggatcaagttttgatgttaaagatgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC

Basic information

species Arabidopsis thaliana
transcript AT5G49460.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 2
---------gtaacataacaatttacattgtctagt-tttca-gttggtttggatcaagttttga--tgttaaagatgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
          |  | || |||| |    |    | | || || |||| ||    |    || |    || | |   |  | |||||| | |||  | ||||| ||||||||||||||||| || |||||||||||||| || ||||| || || || || || || || ||||| || || || |||||| |
gtacgctgtctgtcttatcaatattggctaagaaatgttgcacgttgtttcttttttgcttcttgcttgctgaccttactctgcttt-atagGGAGAGAAACACCTTCTGTTGCTGGAATAATCAATCCTGGTTCTGATGGGTTTCAGAAACTTTTCTTTGGACAAGAAGAAATTGCCATTCCAGTTCATCC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G033226_T01 (Zea mays), 3'ss of exon 2
-------gtaacataacaatttacattgtc-tagttttcagttggtttggatcaagttttgatgttaaagatgatttgctt--ttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
         |||    || | |   ||  | | |||    |  | |   ||   | || |    |||  ||     |||||  ||| |||  | ||||| ||||||||||||||||| || |||||||||||||| |||||||| || || || || || || |||||||| ||||| || |||||| |
gtacacatcaactcttcattctttgttaacatggttgaatggcgttcctgacttacttattcc-ttactgactccgtgcttctttatagGGAGAGAAACACCTTCTGTTGCTGGAATAATCAATCCTGGTTCTGATGGTTTTCAGAAACTTTTCTTTGGACAAGAGGAAATTGCTATTCCGGTTCATCC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G36840.1 (Glycine max), 3'ss of exon 3
-----------------------------------gtaacataaca-atttacattgtctagttttcagttggtttggatcaagttttgatgttaa-agatgatt------tgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                                    ||   |  || | | ||| |  | | |||     |  | |  ||    |||| || ||||  || |||       |   ||  ||||  | ||||| || |||||||||||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||| || ||||| ||||||||
gtgtgtatcaccaactttatcatatcaaattcttactattcttccagactgacagtagcaaatttgtgtgttatattaatgtgcttttaatattaatggaagatcctattatatattcgcagGTAGAGAAACACCGTCTGTTGCTGGAATAATTAATCCTGGTTCTGAGGGATTTCAAAAGCTCTTTTTTGGTCAGGTGGAAATTGCCATCCCAGTTCATGC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G03700.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtaacataaca-atttacattgtctagttttcagttggtttggatcaagttttgatgttaaaga-------tgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                                    ||   |  || | | ||| |  | | |||     |  | |  ||    |||| || |||| |        |  |||   ||  ||||  | ||||| || || ||||||||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||| || || || ||||||||
gtgtgtatcattaactttatcatattaaattcttattattcttccagactgacagtagcaaatttgtgtgttatattaatgtgtttttaatattaatggaagaccctattttttattcgcagGTAGAGAAACACCGTCAGTTGCTGGAATAATTAATCCTGGTTCTGAGGGATTTCAAAAGCTCTTTTTTGGTCAGGTGGAAATTGCCATTCCAGTTCATGC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G15020.1 (Glycine max), 3'ss of exon 2
-----------------------------------gtaacataacaatttacattgtctagttttcagttggtttggatcaagttttgatgttaaagatgattt-gcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                                   |    ||  ||    |   |   | |   | | |   ||||  |  | |  | |||  |    | |||| |  ||| ||||  | ||||| || || ||||||||||| || || ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| ||||||||
gtttgggctggctctatcatcctcattttcttctaggcggattgcagaaaatgatacattgacattaat--atttgcttttaatactaatggaagctctaattttgtgtttgcagGCAGGGAAACACCATCAGTTGCTGGAATAATTAACCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTTCATGC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G04000.1 (Glycine max), 3'ss of exon 2
-----------------------------------gtaacataacaatttacattgtctagttttcagttggtttggatcaagttttgatgttaaagatgattt-gcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                                   |    || |||    |   |   | |   | | |   ||||  |  | |  | |||  |    | |||| |  ||  ||||  | ||||| || || ||||||||||| || || ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| || |||||
gtttgtgccggctctatcgtcttcgttttcttctaggcggattacagaaaatgatacattgacattaat--atttgcttttaatactaatggaagctctaattttgtgttcgcagGCAGGGAAACACCATCAGTTGCTGGAATAATTAACCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTGCATGC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 1
-------------gtaacataacaatttacat-tgtctagttttcag-------ttggtttgg-atcaagttttgatgttaaagatgat-------------ttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
              || |||    |||| | | |     | || |||       |   ||||  || ||  |||| | ||||   | ||             |||  ||   |||  | ||||| || || ||| ||||||| || |  ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| ||||||||
gtttgtataggctctatcatcttgattttcttctaggcggattgcagaaaatgatacatttgacattaatatttgttcttaatactaatggaagctccaattttgtgttcttagGCAGGGAAACACCATCAGTTTCTGGAATAATTAGCCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTTCATGC

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S35_384V6.2 (Physcomitrella patens), 3'ss of exon 2
--------------------gtaacataacaatttacattgtctagttt---tcagttggtttggatcaagttttgatgttaaagatgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                     |   ||   ||| |        ||| |    ||||    | | | ||  |     || || |   | ||| |  | | ||||| | || || |||||||| |||||  | || || || || ||||| ||||| |||||||||||||| ||||| |||||||| ||  |||| || |||| 
agttaagctgtttccgtacttttttattttaatgtgtgccaaatagctggcatcagaaactcttgttcttgacgccatcttgaccgtaattgg--tctgcagGAAGAGAGACTCCTTCTGTGGCTGGTGTAATCAACCCAGGATCTGATGGTTTCCAAAAGCTCTTTTTTGGGCAAGAGGAAATTGCAGTCCCCGTGCATGG

upper sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S46_63V6.4 (Physcomitrella patens), 3'ss of exon 2
------------------gtaacataacaatttacattg--tctagttttcagttggtttggatcaagttttgatgttaaagatg-atttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                  ||  | | |     |   |||  | | ||  |       | ||  || |   | | || | |   || |  ||   | |||||| | || ||||| ||||| |||||  | || || || || ||||| |||||||| ||||||||||||||||| ||||| |||||| | ||||| |||| 
tgcaccagtacaaaactggtcgcttcagtgggtctgttgagtttggtgatgctccattgtgcctcgacaatagttgatgagattgtacctgacgtcacagGAAGGGAGACGCCATCTGTGGCTGGTGTGATCAACCCAGGATCTGATGGTTTTCAGAAGCTCTTTTTCGGGCAAGAGGAGATCGCTGTACCTGTCCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttcagttggtttggatcaagttttgatgttaaagatgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC
                        ttttgat  putative branch site (score: 4)
                                          tttgctttt  putative PPT
                             atgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacataacaatttacattgtctagttttcagttggtttggatcaagttttgatgttaaagatgatttgcttttacagGACGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA