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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG

Basic information

species Arabidopsis thaliana
transcript AT3G46440.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
       | | | | |   | ||   | |    |||   | ||| || | |        ||| |  || ||||| ||     || |  |||    |   ||| |||||| ||||| ||||| || || |||||||| ||||| ||  | |||||||| |||||||| |||||||| || ||||||||||| || ||  | ||
-------gtaatatttttagttcatacct----ttttgtcttgtgatgtac-----tggattgtagttctccttaat-----aagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 8
gtaa-gttgcatttt---ctcaggctctcgcttcaactt-tctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  || |    | | ||  |  |||| |   |||  | |  |   |    || |  ||| | |     | | ||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||| | |||||||| || |||||||||||||| |||||||||||||| || ||  | ||
gtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
gtaa-gttgcatttt---ctcaggctctcgc--------ttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  ||              |||   | |||  ||| || || || |   |   || ||  |  ||| ||| | | | ||||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||  | |||||||| ||||||||||||||||| |||||||||||||| || ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtg-ataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 7
gtaa-gttgcatttt---ctcaggctctcgcttcaactttct----ccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  ||      | |           |||| |   ||   | |  |   |    || |  ||| ||  | | | | ||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||  | |||||||| ||||||||||||||||| |||||||||||||| || ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 4
gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
   | ||  | ||    |   |      |||     |||  ||| ||  | || |   |   || ||  |  |||  || | | | | ||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||  | |||||||| |||||||| |||||||| |||||||||||||| || ||  | ||
---acttaaacttcaata--ttagtagctcatagccctctttgttatgag-ataactctgggcttatgatttttt--tcttaacagtatttatcatctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
gtaa-gttgcatttt---ctcaggctctcgcttcaactttct----ccctgtaatttgcatcaacatattctcattgtcctttattccttaa-attgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  ||      | |           |||| |   ||   | |  |   |    || |  ||| || |||||   | ||| |  |   | | |||||||||||| ||||| || || || ||||| ||||| ||  | |||||||| ||||||||||||||||| |||||||||||||| || ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 5
gtaa-gttgcatttt---ctcaggctctcgcttcaac--tttctccctgtaatttgcatcaacatattctca--ttgtcctttattccttaa-attgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  ||      | |     |  |  |  |  ||   || |    | |||    || |  ||| || ||||| | | ||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||  | |||||||| |||||||| |||||||| |||||||||||||| || ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatcatctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 9
gtaa-gttgcatttt---ctcaggctctcgcttcaactttct----ccctgtaatttgcatcaacatattctcattgtcctttattccttaa-attgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGG-TCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
||||   | ||| ||   || |  ||      | |           |||| |   ||   | |  |   |    || |  ||| || ||| | | | ||| |  |   | | |||||||||||| ||||| || || || ||||| |||||  | | | |||||||| ||||||||||||||||| |||||||||||||| || ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
-------gtaagttgcattttctcaggctctcgcttcaactt-tctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctt--tgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
        |    | | ||| ||     | ||   |||  || | | |   ||    | |   |  |||  |  ||   ||| | |||||    ||||| ||| || | |     ||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||||||| ||
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtt--tcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 9
-------gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtccttta-ttccttaaattgtttttgtttcttctt--tgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
        |    |   ||| || |   | ||   ||   ||  |    | |  |   ||  | || || || ||||  ||||  ||||| |  ||||| | | || | |     ||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||||||| ||
gtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaatagagat-ttttctttgttttttaactccttgaggtgtttatatatcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGCAACTTCATTGCTCAAGCACTGCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
-------gtaagttgcattttctcaggctctcgctt-caactttctccctgtaatttgcatcaaca-----tattct-cattgtcctttattc-----------cttaaa-------ttgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
        | |  |  ||||| ||    ||||  |  |||| |        |     |||  ||||       || | || ||   || | |            || ||        || ||||  | | ||  |   |||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || ||||||||||| |||||| | ||
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 8
---------------------------------gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctt-tgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
                                 ||   |||   ||  |       | | |     ||  ||| ||| ||       |  | ||| || ||    |   ||   | | || ||| | ||||||      ||||||| ||  |||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||||  | ||
gtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttt--tgtaagttaactgagttttttatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCACGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCGATTCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
---gtaagttgcattttctc------aggctctcgct--tcaactttctccctgtaa----tttgcatcaacatattctcattgtcctttattccttaaa----ttgtttttgtttcttctttgt-agAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
    |   ||   |||||||      |   ||||  |  | |     |   | |||     ||||||    | |   || ||   |  | | ||  |       || ||||  ||| || | | | |||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| || |||||||| || |||||| | ||
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 8
gtaagttgcattttctcaggctctcgcttca-actttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttcttt-----gtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
    ||    | |||||    | |  ||||| | ||      ||    |||    |||   |    ||| | || | |   |||| |   |||| | | ||  ||      ||||||| ||  |||| |||||||| ||||| ||||| || |||||||| || |||||||| |||||||| |||||||||||||| |||||| | ||
----gtaatttcttctcttcttttttcttcatagttgtctgttgctccttgttataactggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCGCGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCAATTCG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
       | |  || |  |  | |   || ||       |||| ||    | ||||   ||    ||     |||| |   ||  |||||| | | | || |    |||||| |||||||||||||| |||||||| ||||| || |||||||| || |||||||| |||||||| ||||| ||||| || |||||||| ||
-------gtaacttttgtgtttttttttttaat------cctg-aacaaacttcaatgaat----atgaagttttaatatgtatgttgtttctttatattttggacagAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG

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|47831999|gb|CK121683.1|CK121683
EST:     GCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG                         AAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCG
genomic: GCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgca ... ttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
                                ttgtttttgtttcttc  CT-rich tract
                   tttattccttaaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA