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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaaatcatttctaactctagttatcatgtatacttatatatatgacttacttcatgaaatcaaatcatcatcttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG

Basic information

species Arabidopsis thaliana
transcript AT1G80830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 11
------------gtactaaaatcatttctaactctagttatcatgtatacttatatatatgacttacttcatg--aaatcaaatcatcatct-taaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
             | |  || |  ||  | ||   ||   |  | | |   |   | | || | |||    ||   || |   || |  ||| |  | |||||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||  ||||||||||||||||  ||||||||||| | |    |
tttgtgtatggtatgcataattttttgtttacaacagagttggtctctggctcc-tctctgccataccatgtgctgaagcccttctttgtctattcatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAGATGGGGACACATGTCAACTCTACCATG

upper sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G44710.1 (Glycine max), 3'ss of exon 10
------------gtactaaaatcatttctaactctagttatcatgtatacttatatatatgacttacttcatg--aaatcaaatcatcatct-taaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
             | |  || |  ||  | ||   ||   |  | | |   |   | | || | ||| |  ||   || |   || |  ||| |  | |||||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||  |||||||||| |||||  ||||||||||| | |    |
tttgtgtatggtatgcataattttttgttcacaacagagttggtctctggctcc-tctctgccataccttgtgctgaagcccttctttgtctattcatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAAATGGGGACACATGTCAACTCTACAATG

upper sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
---------gtactaaaa----tcatttctaactctagttatcatgtatacttat-atatatgacttacttcatgaaatcaaatcatcatcttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
         ||| | | |     | | | | |  | | | | | |||    |||| || |  |   ||  |  |||| ||      |        | |||||||||||||| |||||||| || ||||| ||| |||| || ||||| ||||| ||  |||||| |||||||||   |||||||||| ||||  ||
tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG

upper sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 12
-gtactaaaatcatttctaactctagttatca---tgtatacttatatatatgacttacttcatg----aaatcaaatcatcatcttaa------aacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
  | || ||  |  ||  |  || |  ||      | | | || || | |||   |||  || |     ||| | || | |     ||         |||||||||||||| ||||| ||||| |||||  |  |||| |||||||| ||||| || ||||| || ||||||||| || |||||||  | |    |
gtttctcaacacggttacatatccacatagagaattttttgctcatgtctattttttagctcttacggaaaacctaacctttgatgtattgtcttggcagATGATCTTATCATTTGAACTCCCTTTTGCTCTCATTCCACTTCTCAAGTTCACCAGCTGCAAGACTAAGATGGGTGCATATGTCAATTCGACCATG

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|86085916|gb|DR381675.1|DR381675
EST:     CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCG                         ATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTAAAATTC
genomic: CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCGgtactaaaat ... cttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTC
EST: gi|116476122|gb|EG518714.1|EG518714
EST:     CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCG                         ATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTC
genomic: CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCGgtactaaaat ... cttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTC
EST: gi|116476120|gb|EG518712.1|EG518712
EST:     CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCG                         ATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTC
genomic: CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCGgtactaaaat ... cttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTC
EST: gi|124873543|gb|EH955188.1|EH955188
EST:     CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCG                         ATGATCTTATCCTTTGAGCTCCCGTTTG
genomic: CTCTCATCGGTGGTTCAGCTGGAGCTGGAAAGTTAATCATCATTGCCTCGgtactaaaat ... cttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatacttatatatatgacttacttcatgaaatcaaatcatcatcttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
                 gacttac  putative branch site (score: 2)
                                         tcatctt  putative PPT
       ttatatatatgactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaaatcatttctaactctagttatcatgtatacttatatatatgacttacttcatgaaatcaaatcatcatcttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG