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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

Basic information

species Arabidopsis thaliana
transcript AT4G38510.5
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------------------------gcaagtctcgcaatcacactacagacatc--ttgaagcaaattttagttccaatgtttt--tctgaaggtttct--------cattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                                                                                  | | ||   ||     || |  ||||  ||  | || |  ||      | ||||       |||  | | |        ||  ||  | |    ||||||||| || ||||| ||||| ||||||||||| ||||| || ||||| |||||||| || || ||||||||||||||||| ||||| || ||||||||  
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 8
---------gca-agtctcg---caatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
          || | ||  |   ||||||   |  | |  |     |   | | |    | ||   | ||| | |    |    ||||| | |     |||||| ||||||||||| ||||| ||||| ||||| ||||| || || || ||||| || || || ||||||||||||||||| |||||||| ||||| ||  
cccctgcacacataatcatgagccaatcattttctaaatttgacataattagtgtataatacagcatatttttaacacctca--attctctctgttttacagGCTAACGACCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCGGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTTATCT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
------gcaagtctcgca--atcacactacagacatcttgaagcaaattttagttccaatgttt--ttctgaaggtttct--cattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
       |  | |  |||  |  |     || | || ||  | ||  |   |    || ||| |    | | |  ||| |  ||   || |   |  |||||| || || ||||| ||||| ||||| ||||| ||||| || || || ||||| || || || ||||||||||||||||| |||||||| ||||||||  
ctatcctctggccctgcataacgatgagccaaatatattcta-catgtgacataatcagtgtatagcacagcatatttttaacaccttgatcctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 8
-------gcaagtctcgcaatcacac-tacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcatt-ctgttttccgc-acagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC-
          | | |   | |  ||  |   ||  || |||     ||    |  |  ||  ||        || |||  || ||||  |     ||||||||| || || || |||||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||||||||| ||||| || | 
gtggatgatcattgtgctatttgcaaattttgatttcatgacctgtatgaaggagctgatcattaaaatcctgtctcttgttgctgtgatttattacaggCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATACT

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 8
----------------gcaagtctcgcaatcacactaca-gacatct-tgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                |  | | ||  | |   | | || ||| | | ||||| || |  |  ||  ||| | | |||     ||| |   | || ||     | ||||||| || || || |||||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||||||||| ||||| || |
tgtggattatcattgtgttattttcaaattttgatttcatgacctgtatgaaggaactgatcattaaaat-tctctct-----tttgttgctgtgattcat-tatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCATATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 9
---------------gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                 | |  |    ||  |   ||   |||   | ||| |||      |  |||||| |  ||    | |     | || ||| |   |||||||| || || || ||||||||||| |||||||||||||| || ||||| |||||||| || ||||| ||||||||||||||||| || ||||| || |
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaaggagctaatccc---taaaatgttctcttgctaatgtgaatatgtgatttac-tgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCACGTTCTTGTGATAC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
----------gcaagtctcgcaatcacactaca-gacat-cttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
            || |   ||  |   | | |  ||| | | ||||| |  |  |   |  |||||| |  ||    | |     | || ||| |   |||||||| || || || ||||| ||||| |||||||||||||| || ||||| |||||||| || ||||| |||||||||||||||||||| ||||| || |
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttac-tgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                                  |    | |   |   | | |  | || || || ||   || ||      ||  |||   |  |||||| ||    |     | |||||| ||||||||||| ||||| || |||||||||||||| || || || || |||||||| || || ||||||||||||||||| ||||| |||||||| |
gtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaa-attttaaaccaggcttcagaatagttggctttg-aatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
-----gcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggttt----ctcattctgttttccgc--acagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
          |||  || || | ||       || |  | ||| || |      | | || |  | |   |||       | ||| | ||  ||   ||||| || || || || ||||| || || ||||||||||| ||||| ||||| |||||||| ||||  || ||||||||||| ||||||||||| ||||| |
aaatcaatgttcttccattccctctttctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
-------gcaagtctcgc---aatcacactacagacatcttgaagcaaattttagttccaatgtttt-tctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
        |||  ||| |     || |  ||   |  |    ||   | |  | |  | ||  |||  | |     |||   |||     |      ||||| || || || || ||||||||||||||||||||||| || ||||| || |||||||| || |  || ||||| ||||| ||||||||  | ||||| |
catgtttccaaccctctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------gcaagtctcgcaatcacacta---cagacatcttgaagcaaat---tttagttccaatgttt--ttctgaaggtttctc-----attctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                                                                                                 |   || | |  |   ||| |   ||    || |  ||    |   |||  ||||    ||   ||||| |  ||| |      ||  | ||   |   ||||| || || || || ||||||||||| ||||| ||||| || ||||||||||||||||||||||  || ||||| ||||| ||||| || || ||||| |
gtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcagGCTAATGATCCAACAATTGAGCGTATTATCACACCTCGAATTGCACTTACAACTGCTGAGTACTACGCTTATGAGTGTGGAAAGCACGTTCTGGTCATCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164097611|gb|ES030150.1|ES030150
EST:     GTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: GTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
EST: gi|86066802|gb|DR362559.1|DR362559
EST:     ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
EST: gi|163992106|gb|ES203115.1|ES203115
EST:     TTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCA
genomic: TTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTT-AACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCA
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC
                               tttctcattctgtttt  CT-rich tract
               aatgttttt  TA-rich tract