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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctttgtcaatattatcttttgtagaaacctgacatttcgttccatgtgaaatgctcatgctgtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

Basic information

species Arabidopsis thaliana
transcript AT2G20840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
--gtatctttgtcaatattat-cttttgtagaaac--ctgacattt-cgttccatgtgaaatgctcatgctgtca------tctttattttggt----agCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
   |||  |||  ||| || | ||| |||     |   ||  || |   |||||| | |  || |  | ||| |       ||||| ||||  |    ||| || ||||| || |||||||||||||||||||| || || ||| | || |||||||||||||||||||||||||| ||||| || || || || |||||
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
-----------gtatc-tttgtcaatattatcttttgta-gaaacctgacatttcgttccatgtgaaatgctca--tgctgtcatctttat-tttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
            || | |||||   || | |  |   || ||  ||    |    ||| | |   |  |  | |  |    ||| | || | ||| | ||| || ||||| || ||||| ||||| |||||||| ||||| |||||||| || ||| | ||||||||||||||||| || ||||| || ||||| || ||
tgcattgtctgctagcatttgtttctactgttgtagctaagatgccctttacaaagttgcttactatttatttacctaacttcacccttctcttttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
----------gtatctttgtcaatattatcttttgtagaaacct-----gacatttcgttccatgtgaaatgctcatgct-gtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
          | ||   ||    ||  |     || ||||| ||     |  || |  ||| |  |      || |   |  | |||||   | |   ||| || |||||||||||||||||||| ||||| || ||||| || |||||||| ||||||||||| ||||||||||| |||||||| || || || |||||
agaatcagttggattggtggtggtaaaacaccctgaagaaatctcggttgctatatatttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
-------------gtatctttgtcaatattatcttttgtagaaac---ctgacatttcgttccatgtgaaatgctcatgct-gtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
              || | |   |   |  | | |    | | |     ||  || |  ||  |  |      || |   | |||||||||  |||   ||| ||  ||||||||||||||||||||||||| || ||||| || |||||||| || |||||||| ||||| ||||| |||||||| || || || || ||
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttatttt-cagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 5
----------------------------gtatctttgtcaatatt----atcttttgtagaaacctgacatttcgttccatgtga-aatgctcatgctgtcatc--tttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
                            ||  |||||  |   ||     || ||       ||    | |||||||     | | ||| |       || |||  | |  | | | ||| ||  ||||| | |||||||||||||||||||||||||| ||  |||||||| | || |||   || ||||||||  |||||||||| || |  |  ||
gtggagtttcagagtgtcatcatccgacgtcgctttgctatcttttggcgtcattcacgaggactc--cctttcgttaatgataataatacgagcatcgttatccatctcctcttgcagCTGGCGTTGTGTTGGAAGAGAAAAACTGGCCACCGTTTTTCCCCATCATCCATAACGATATTGGCAACGAGATACCTGTCCATCTGCAAAGTACACTGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G124938_T01 (Zea mays), 3'ss of exon 4
gtatctttgtcaatattatcttttgtagaaacctgacatttcgttccatgtgaaatg-ctcatgctgtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
|||    | | ||| || | ||||      |  |  |||||  ||| |  ||||||| | |||    | |   || | |  | ||| ||| || | |||||    ||||||||||||||||| || ||  |||| |||  ||||||||||||||| |||||| | ||  ||||| || | || ||
gtaataatcttaattttgttttttt---gcatgtaccattt--ttcta-atgaaatggcccataaatttaaaattttatatgcagCTGGAGTTTTAATAGAGCCCAAAAACTGGCCACCGTTCTTCCCCGTCATTCATGTTGACATTTCAAATGATATACCCGTGCACTTGCAGCGAGTGCAGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 5
gtatct--ttgtcaatattatcttttgtagaaacctgacatttcgttccatgt-----gaaatgctcatgctgtcatctttatt-ttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
|||| |  |||     |     | || |||||| |    |    | |   |||     |   |  | ||    | || |||    || | ||| ||||| || ||||| |||||||| |||||||| ||||||||  |||| |||||||||||| |||| || ||||| || ||||| || || ||||| ||
gtatttgattgagttcacctattcttatagaaatcaactagagtgatgtctgtattttggtgttttaatttatttattttttccatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTTCCCATCATTCATCATGACATTGCAAAGGAAATACCAATACATCTTCAAAGGATCCAGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
gtatctttgtcaatattatcttttgtagaaacc---tgacatttcgttc-catgtgaaatgctcatgctgtcatctttattttg-----gtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
|||| |  ||  ||  |||  ||| |||||| |   |    |   ||    || |    | || |     | || ||| ||||      | ||| ||||| || ||||| |||||||| |||||||| ||||| ||  |||| |||||||||||| |||| || |||||  | ||||| || || ||||| ||
gtatttgagttcat-ctattctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

upper sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
gtatctttgtcaatattatcttttgtaga------aacctgacatttcgttccatgtgaaatgc--tcatgctgtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
|| | | |||   |  |||| || ||  |      |   |||    |  || ||||     | |  ||    | ||||  ||  ||||| ||| |||||||| ||||| |||||||| |||||||| ||||| || || || |||||||||||| ||||||| ||||| |||||||  ||||   | || ||
gtttgtctgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctgacatttcgttccatgtgaaatgctcatgctgtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA
 acctgac  putative branch site (score: 3)
                                        tctttatttt  putative PPT
                                       atctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctttgtcaatattatcttttgtagaaacctgacatttcgttccatgtgaaatgctcatgctgtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG