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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC

Basic information

species Arabidopsis thaliana
transcript AT2G21410.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 10
caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttg-atcac-tacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
 ||      |||  | ||  |   |   |   |   |  |  ||||| || |      |   ||   |   |        ||||| || || |    | |||  | ||||||||||| || || || ||| |||||||||| ||||| || || || ||| | |||||||| |||||||| || ||||| |||||||| |||
-aattagcattgactcctgaaaaatcaataaagagcttgctgtttgt-ttgggccaaatggtttagttaggaactgctaactttgtattacatctgatacagGATAGCCAAATATCAAGAAGCAAACCCTGGTGTATTCACTATTGTCACTTTTCCTTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttc----tttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
   | | | |    ||  | |     | |  | || ||||  ||   ||| |  |   |    | |  |  ||   |  |     | || ||  |    | |||||| ||||| ||||| || || |||||| | |||||||| ||||| || ||||| ||| | |||||||| ||||||||||| ||||| |||||||| |||
---cttatatcttgtaaataaagaagtgtaattca-tatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
-caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
   |  |||  |  |||    | |     |  ||  || |    ||  | |   |   ||    || ||    ||    | || || ||  |    | |||||| ||||||||||| || || |||||| | |||||||| || || || ||||| || || ||||| || ||||||||||| ||||| ||||| || |||
cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataa-gtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
-----caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtct-cttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
          ||| |  |    ||||    |  ||    | |  |   |||  ||| || |  ||| | || |  |||   ||  || || ||    || |  |||  | ||||| || ||||| || |||||  |||||| ||||||||| || || || ||||| |||||||| ||||||||||||||||| ||||| || |||
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactca--aataatcgttaat----acttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 10
caacctttcttgcttactttattttttcttctgcaatatccatttg--tgttagtgttcgtctct-tgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
      |||||    | || |    || || ||| || |   |||   | ||| | ||    | | | ||| | ||   |   |||| ||    | ||| ||| || || || ||||||||||| ||||| | ||| |  ||  | |||||||| || || || |||||||| ||||||||||| |||||||||||||| || 
---ttattcttaacaatttaagaacttgttttgctattttttttttacttttatttttgaaatatatcaatcttatactttaacttttatactaatatttcagGGTTGCTAAGTATCAGGAGGCAAATCCGACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGTCATGGAATATGT

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 10
--caacctttcttg--cttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
   |||  ||   |  |||  || ||| ||| || |  | | |   ||| | || |   |  | ||   ||| | ||   ||  |||| ||    ||||| ||| || || || ||||||||||| ||||||| ||| |  ||  | |||||||| || || || |||||||| ||||||||||| ||||| |||||||| || 
cctaacaatttaagaacttgtttcattatttgttttttacttttattttttatttgaaat-atatc---aatcttatacttcaacttttatactaacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGT

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 10
----caaccttt-cttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctct-tgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
    |||| | | || |   | ||||| | || |  |  | |  |   |||  ||| || |  ||| | ||||  |||   |    ||      ||||| |  |||  | ||||| || ||||| || |||||  |||||| |||| |||| || || || ||||| ||||| || ||||||||||||||||| ||||| || |||
ggtacaacttgtactagtggattttatatgttttcgtttagttgcttcttgatttattgataatctgtctgaaactcaaataatcgct------actacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAGTTGTCACGTTTCCATTCCTTTTTGCCGTAATGTTTGGTGACTGGGGGCATGGCATATGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgat--cactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
 |   |   ||      |||  ||||  || |||   ||    |    |||       |   |||  |   |   |  || | ||||  || |  ||||||| |||||||| ||||| ||||| |||||| |||||||||| |||||||| || || || || |||||||| ||||||||||| ||||| |||||| | |||
tattttactttaacctatttgattttcattttgctg-atgatatcaaattaacaga-attgtttgcctcatactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
caacctttcttgcttactttattttttcttctgcaa-tatccatttg--tgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
      || ||  | |  |  | ||  | | |  || ||      |   ||||   ||       |  |||   |  ||||  ||      |  | ||| ||| |||||||| |||||||| |  |||||| |||||| |   ||| |||| ||||| ||||| |||||||| ||||||||||| ||||| |||||||| |||
---ttgttatttttcaaatggtattgccctatagaagtacttggctaaatgtttaagtggcatcatccaatagtagagatcaactaattcaataatatttcagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S60_200V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtg-----ttcgtctcttgaatttcatggatcttctttgatcactacat-tgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
                                     |  ||  ||    ||   |   | |   |      ||   | ||||   | ||     ||  | |||  |   |||     |    |  |   |||||| |||||||| |    ||||||||| || || ||| |    || || ||  | || ||||||||||||||||| || ||||||||||| ||||||||||| || || 
gtcagtgttcacacaccaatgttagtctgacatgtgaatgctgcctcatctatggtggctctatctagctggtaaggaattgtagcattggatgatttttttctccacactcaactgacaaggtgaaattctacatgtgcagTGTAGGACGATATCAGGAAGCAAACCCTGGATGTTTTACTATCATAACATTCCCCTTCCTGTTTGCGGTAATGTTTGGTGATTGGGGTCATGGTATTTGT

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S115_183V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------------------------------------caacctttcttgcttactttattttttcttctgc--aatatccattt---gtgttagtgttcgtctctt---gaatttcatggatcttctttgatcactacatt----gcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC-
                                                                              | || |    ||   |  || |      |   |    | ||| |      || | ||     |  | ||    ||||      |  || |||    || |  ||    | || ||||| |  ||||| || || || ||| |    ||||| || ||||| ||||| ||||| ||||| ||||||||||| |||||||| ||||| ||  || 
gtaagtttcaacaaaacatgtcgatggaaataggaattccaagaaatctagagtaggcatttttcgatcgaatacaaacgacatacactgtgaatcttttcaaagatcgaggcagagatcaaagcagagtctaaggaccagcatgttcaaaaattctgaacacattatttacataccagcttttgtgtagGGTGGCAAGGTATCAAGAAGCGAACCCTGGATGCTTCACGATCGTTACATTCCCATTCCTCTTTGCGGTTATGTTTGGCGACTGGGGACATGGCATA-GCA

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------caacctt-tcttgcttactttatttttt--cttctgcaatatccatttgt-----gttagtgttcgtctcttgaatttcatggatcttctttgatcact---acat-tgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
                    ||   | ||  |   |   |  | | |   || ||| || |  |  |||     | | ||| || | | ||   ||   |    |     |||||| |   |||| | ||| ||||     ||||||||||| |||||| ||   || || ||  | || || || |||||||| ||||||||||||||||||||||| ||||||||||||
gtaggtgtggtgatcagtataattatgtcgaggagaagctggtctgtgatttttgctatttttaactgtcaagcgattgtggtcatatttttgcttctttcacacggtactgatcatttaaacatgtacagAGTGGGGCGGTATCAGGAGGCAAATCCTGGTTGTTTTACCATAATAACATTTCCATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGC

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtct-cttgaatttcat--ggatcttctttgat--cactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
                                   || ||   ||| | |   |   | || |       ||     ||||| || || | || | | |   ||||||   | |||  |  |||      |   ||||||||||     |||||||| || |||||| |    || || ||  | || ||||| ||||| || ||||||||||||||||||||||| ||||||||||| 
gtaagtgtgcagatcaacgatattacgacgcgttgaaactgggttgttgatgatcgctgttttcaactgctaagggattgtggtaatggttgttttcctttctttcattcagttctgatcagatgttgtgaatatgcagTGTGGGACGGTATCAGGAAGCAAATCCTGGATGTTTTACCATAATAACTTTCCCTTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGT

upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------caacctttcttgcttactttattttttct-------tctgcaatatccat-ttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
                                     || ||   ||   ||   | | | |||        |  | ||| |   |   ||||   | |   |||| |       || ||       |  |    |    |||||||||     ||||||||||| |||||| |    || || || || || |||||||||||||| ||||||||||||||||| ||||| || || || |||
gtcagtgtccatacacctatgtaactttggcatctagaaactgaattctatatgatgtctattccaagcggataaggaatctttgtaccgtgtgcttttcgttctcctatgcacaattgacaaggggttgttgaaaatgcgcagTGTGGGGCGGTATCAGGAGGCAAATCCTGGATGTTTTACTATCGTAACGTTCCCCTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGC

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|116483494|gb|EG526086.1|EG526086
EST:     CGCACAAACAAATTTACTACTGCTTTCCAGGAAATTGTTGATGCATACGG                         TGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTT
genomic: CGCACAAACAAATTTACTACTGCTTTCCAGGAAATTGTTGATGCATACGGgtaagcatct ... tacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTT
EST: gi|125224751|gb|EL238836.1|EL238836
EST:     TTTACTACTGCTTTCCAGGAAATTGTTGATGTCATACGG                         TGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCT
genomic: TTTACTACTGCTTTCCAGGAAATTGTTGATG-CATACGGgtaagcatct ... tacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCT
EST: gi|124737209|gb|EH828611.1|EH828611
EST:     TTTACTACTGCTTTCCAGGAAATTGTTGATGCATACGG                         TGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTT
genomic: TTTACTACTGCTTTCCAGGAAATTGTTGATGCATACGGgtaagcatct ... tacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC
                                   ctttgat  putative branch site (score: 5)
                 ttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- -cctttct
- - - - - - - - - - - - - -cttctgc