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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaactctgaaatatagttatgtgatgatgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC

Basic information

species Arabidopsis thaliana
transcript AT3G49690.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g56090.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------gtacta--ttcatatacgttattcatgtatatatcgttaaaatatcatgtggaa----actctgaaatatagtt--atgtgatgatgtctata-attaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
                                                                | | ||  | |  |  || ||  || | |   |   |  | ||      ||  |    | |   |  |||  |   |  |||  || | |  |    | |||||||| ||||| || || ||  ||||||| || || ||||| || || || ||||||||||||||||||||||||||||| ||| ||  ||| ||    
gtatacttgctaattcagctgggcacacacaagtctagtcactcctatgatcaactcaactgtagaattagctgcgaaaccggtaggcaggcaggcaggttgcacatggggcatgagagtgtagtacaatctatgatctgacatgaccatatatgcatggcacagGTGGTCGATAATAGCAGCGCAGCTGCCGGGGCGGACGGACAATGACATCAAGAACTATTGGAACACGAGGCTCAAGAAGAAGCTCTTTGGCAAGCAGTCG

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104789_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaactctgaaatatagttatgtgatga--tgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
                                                                                      |  ||  ||   || | || ||||  | | | |        |   ||  |  || |||  |  | | |   ||  |    |  ||      |||||||| ||||| || || ||  |||||||| | || |||||||| ||||| ||||| ||||||||||||||||||||||| ||| |   ||| ||    
gtaaagttcagtagctaggtcgtcctgacctggtgttttcttcgatcaaatccacacactgtagaatttgctggctgcaaaccaactgttaggcacgcacatgatgcatgggtgtgt-gcccggccgtagagtctac-ctatgacctgaactgaacggaccagtcatgcatgcccgtagGTGGTCGATAATAGCGGCGCAGCTGCCGGGAAGGACGGACAACGACATAAAGAACTACTGGAACACGAGGCTCAAGAAGAAGCTCTTCGGCAAGCAGTCG

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104789_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaactctgaaatatagttatgtgatga--tgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
                                                                                      |  ||  ||   || | || ||||  | | | |        |   ||  |  || |||  |  | | |   ||  |    |  ||      |||||||| ||||| || || ||  |||||||| | || |||||||| ||||| ||||| ||||||||||||||||||||||| ||| |   ||| |     
gtaaagttcagtagctaggtcgtcctgacctggtgttttcttcgatcaaatccacacactgtagaatttgctggctgcaaaccaactgttaggcacgcacatgatgcatgggtgtgt-gcccggccgtagagtctac-ctatgacctgaactgaacggaccagtcatgcatgcccgtagGTGGTCGATAATAGCGGCGCAGCTGCCGGGAAGGACGGACAACGACATAAAGAACTACTGGAACACGAGGCTCAAGAAGAAGCTCTTCGGCAAGCCGTTT

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G05260.1 (Glycine max), 3'ss of exon 2
----gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaactctgaaatatagttatg-----tgatgatgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
      | | |||| | | ||| || |      |||  ||  || || |  | || ||     | | |    |||     || |||||||    |    ||||||||  | || || || |||||||||||| |||| || || || ||||| |||||||||||||||||||| |||||||| ||  |    ||||| || 
gaaaaaaatcttcaaaaa-gttcttgacaatattatttttctaaaataaacttgatacatgtgagtttgacaatgaaccctgttgatgtcatgtaacgcagGTGGTCGGTCATTGCAGCACAATTGCCGGGAAGAACTGATAATGACATAAAGAACTATTGGAACACGAGGCTGAAGAAGAAGCTTCTAGGGAAACACCGT

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA0041S00310.1 (Glycine max), 3'ss of exon 2
-----gtactattcatatacgttat-tcatgtatatatcgttaaaatatcatgtggaaactctgaa-atatagttatgtgatgatgt---ctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
      || || | |||    |||| ||    | ||  | ||   || || |   ||   ||| || | |   | ||  ||  ||      | | || | ||||||||  | || || ||||||||||||||| |||| ||||| || ||||| ||||| |||||||||||||| || ||||| ||  |    || || || 
aaaagttaatagttataacttttatatctcaaacatgac-ttcttatttctttacgagtttctaaacacactatgata-gacaatacatgttgtcatcacagGTGGTCGGTGATTGCAGCTCAATTGCCGGGAAGAACCGACAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G05170.1 (Glycine max), 3'ss of exon 2
--gtactat-tcatatacgttattcatgtatatatcgttaaaatatcatgtggaa---actctgaaatatagttatgtgatgatgtctataattaa--agGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
   || ||| |     |  | |        ||  |  |||| |  |   ||  ||   | | ||| || |  ||  |  ||||   || |  | |   ||||||||  | || || || |||||||| ||| |||| || || || ||||| |||||||||||||||||||| |||||||| ||  |    || |  || 
caatattatatttccaaaataaactgaacttaagtaattaacaggtttagtttaactgagtttgatatttgcttgagcaatgaacccttttgtgacgcagGTGGTCGGTCATTGCAGCACAATTGCCAGGAAGAACTGATAATGACATAAAGAACTATTGGAACACGAGGCTGAAGAAGAAGCTTCTAGGGAAGCGCCGT

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G10340.1 (Glycine max), 3'ss of exon 2
gtactattcatatac-gttattcatgtatat---atcgttaaaa--tatcatgtggaaa-ctctgaaatatagt-tatgtgatgatgt---ctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
    |    ||| || ||  ||||| | |||   |  | ||| |  |||       | |  |   ||| | | | ||   ||  ||      | | ||   ||||||||  | || || ||||||||||| ||| |||| || || || ||||| ||||| |||||||||||||| || ||||| ||  |    || || || 
---tttcagatacacagtctttcatatttattaaaaagctaatagttatttctcaaagagtttctaaacacactataatagacaatacatgttgtgatcgcagGTGGTCGGTGATTGCAGCTCAATTGCCAGGAAGAACCGATAATGACATAAAGAACTACTGGAACACGAGGCTGAAAAAGAAGCTTCTGGGGAAGCACCGA

upper sequence: AT3G49690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S46_302V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaact--ctgaaatatagttatgtgatgatg-tctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC-
                                                              |        | |   ||| |||  |  | |  || || | | |  ||| ||||    | |   | |    | |   ||||  | | | | |  || |||||| | || || || ||  |||| ||| ||||||||||||||||||||||  | |||||||| ||||| ||||| || |||  | |||     |   
gtaccaattgcgctgtagttttgatgctaaccttcggaataaacgtcagtgatgaatgttcagcgtgcacaagaagagttgttcgagggtctg-cggtacattgttttgtagaaatggacagggttcttaccaggaagtgattctttctgagtgcagATGGTCTCTTATTGCCGCACAGATGCCAGGAAGAACAGACAACGATATAAAAAATCACTGGAACACCAGGCTAAAGAAAAAGCTCTGTGACATG-GGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatcatgtggaaactctgaaatatagttatgtgatgatgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC
                                       atgtctataattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattcatatacgttattcatgtatatatcgttaaaatatcatgtggaaactctgaaatatagttatgtgatgatgtctataattaaagGTGGTCTATAATCGCTGCTCAATTGCCGGGACGAACAGACAACGATATAAAAAACTATTGGAACACGAGGCTCAAGAAGAAACTCATTAACAAACAACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA