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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaatacaaaactaacttacttgtagttcttttgtaattaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA

Basic information

species Arabidopsis thaliana
transcript AT5G53950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G34950.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------gtaagaaa--atacaaaactaact-tacttgtagttcttttgtaattaaggtttct-------gaaatcttta---ctctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                                       ||| |     | ||  |||  || || | ||||| |        ||    ||||        | || ||||     | |   | ||    || || ||||||||||||||||||||| ||||||||||| ||| | |||||| ||||||| || || ||  | ||||| || || || ||||| ||||||||
gtaaaattaagcactttcaacgccctttctttttttctttcttatctttggctattaatatttctttcattacttgctatagtggtagtacaaagaagtttggattttccacctaacgtaacctttgtggttgtttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGGAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGTTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G26190.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------gtaag-aaaatacaaaactaacttacttg--tagttcttttgtaattaaggttt-----------ctgaaatctttactctcaatgttactt--------agGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                                                   || | | || | ||  || ||||| |    || |  |  ||   || ||  ||            || ||| | ||   |   | |   ||        || || ||| |||||||| ||||| ||||||||||||| |||||| |||||||| ||||| || || ||  |  | || || ||||| ||||| ||||||||
gtaactaattacaacaacaaaaccaaaaccctcatcgactaattttaagactaaaacaatgtatatatatgtagaaaataactctcacttagtaaaataatcatcatggggttgagaattaggccaaaactttgtaatttctaactttgttatcgtttcatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGGTTACGCACAAATAGAGCCACTGAAGCTGGTTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
----------------gtaagaaaat-acaaaactaacttact-tgtagttcttttgtaattaaggtttctgaaatct-ttact-ctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                |||||| ||| |      |     | | ||        |||| |||      | ||  || |  || |  |  || |     || || ||| |||||||| ||||| ||||||||||||| |||||| |||||||| ||||| || || ||| |  | || || || || || || ||||||||
taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
--------------------------------------gtaagaaaatacaaaactaacttacttgtagttcttttgtaa-----ttaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                       | |  |  | ||    |  ||| ||  ||||     |  ||     ||    ||||         ||  ||   | ||    || || ||||||||||||||||||||| ||||||||||| ||| | |||||| | ||||| || || ||  | ||||| || || || ||||| ||||| ||
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttct-atagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
-------gtaagaaaatacaaaactaacttacttgt--agttcttttgtaattaaggtttctgaaatctttactctcaatgt-tacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
         |   |  |||    |||  ||   | |  |   |      |||  |    | |  |  | ||  | | ||  |  |   ||  | ||| |||||||||||||| || ||||||||||| |||||||| || ||||||||||| || || ||  |||| ||| | || || || ||||| ||
gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------gtaagaaa----atacaaaactaactt----acttgta-gttcttttgtaattaaggtttctgaaatc------tttactctcaatgttact-tagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                                                     ||| ||||    |||| ||| | | |     | | | | | |||   | |       ||| ||  ||        |   |||| ||| |  |  ||  |  || ||| | |||||||| |||||||||||||| || || |||||||| || || || || || | | ||||||||||||| |||||    || ||
gtatttttttcttttcgcattatccttcagaacatttggtgtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcagATAAGGCCAAGGTTGGAGAGAAGGAATGGTACTTCTTCAGTCTGCGTGACCGAAAATACCCAACCGGCCAGCGAACTAACAGAGCCACTGATAAGGGATA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------gtaagaaaatacaaaacta--acttacttgtagttcttttgtaattaaggtttctgaaatctttactct--caatgttactt-------agGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                                                                                          ||| || |   || | |  ||||   |  ||||   | |     |    |    |||||| | || |     | || |||       || || ||| || ||||||||||| |||||||||||||||||| |  | ||||||||||| ||||||||  || | || ||  | ||||| ||||| || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------gtaagaaaatacaaaacta--acttacttgtagttcttttgtaattaaggtttctgaaatctttactct--caatgttactt-------agGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                                                                                                          ||| || |   || | |  ||||   |  ||||   | |     |    |    |||||| | || |     | || |||       || || ||| || ||||||||||| |||||||||||||||||| |  | ||||| ||||| ||||||||  || | || ||  | ||||| ||||| || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
------------------gtaagaaaatacaaa-actaact--tacttgtagttcttttgtaattaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
                   |||        | |  ||| ||  | |||| ||| | |  | | |         |    | ||  ||||   |   ||  ||  |  || |||||||||||||| |||||||||||||| |  || || ||||| |||||||| |||||| || | || ||| |||| || ||||| || ||
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgct-ccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

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|86061083|gb|DR356840.1|DR356840
EST:     TGCCATCGCAGAAGTTGATCTCAACAAGTGTGAGCCTTGGCAACTTCCCG                         GGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC
genomic: TGCCATCGCAGAAGTTGATCTCAACAAGTGTGAGCCTTGGCAACTTCCCGgtaagaaaat ... tgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC
EST: gi|164211203|gb|ES034157.1|ES034157
EST:     CTCAACAAGTGTGAGCCTTGGCAACTTCCCG                         GGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC
genomic: CTCAACAAGTGTGAGCCTTGGCAACTTCCCGgtaagaaaat ... tgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC
EST: gi|86061082|gb|DR356839.1|DR356839
EST:     TGCCATCGCAGAAGTTGATCTCAACAAGTGTGAGCCTTGGCAACTTCCCG                         GGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC
genomic: TGCCATCGCAGAAGTTGATCTCAACAAGTGTGAGCCTTGGCAACTTCCCGgtaagaaaat ... tgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagttcttttgtaattaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
      ttcttttgtaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaatacaaaactaacttacttgtagttcttttgtaattaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA