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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

Basic information

species Arabidopsis thaliana
transcript AT1G51690.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
---ttcaagttcct--atccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
   |   |||||    | || |    ||  | || |  | |    |        ||         | ||||    || ||  |     | || | ||| |   || ||||| || ||||  || || || |||||| ||||||| ||||||||||| |||||||||||||| ||||| || |||||||||||||| |||||||| 
ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaataccatgttctca-----tattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
--ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
  | |   |    |||  |    |||     ||     ||        | |  | ||| || |  | |  |  || | |   |  | ||| | || |    || || || || || || || || || ||||||||||| || |||||||||||| ||||||||||||| |||||||| || ||| ||||||| || ||| | 
tttgctgatgtgcatctca-tatacattcgattagatgtaatgtaccctttcgagttttatgtagtgacatattgttgcc--tgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataatt--agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
   | ||| ||       |   ||  |  |  |  ||| ||  | ||    | |||  |  ||   ||  |  |    ||| | |  |   |||      || || || || |||||||| || |||||||||||||| || |||||||||||| ||||||| ||||||||||||||||||||| ||||||| |||||| | 
--tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
-ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttc--attga-taatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
 | |   ||   | |    |  | | |||     |||     |   || | || | ||  ||||  || || | |  |  || |  |  |  |  | | |  || || || || |||||||| || |||||||||||||| || ||||| |||||| ||||||| ||||||||||||||||||||| ||||||| |||||| | 
ttgctgatttgcacct---cttatatcttaaatgtatgctgccattttttgtattgtcctattgggtagtgatata-tattatttgtaatctttatttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
|  | |     ||      |      || | ||| |||  |   | |   |   || |||  ||  ||  | |           ||| | || |    ||||| || ||||| || || || || |||||| ||||||| || ||||||||| | |||||||||||||| || || || ||||||||||| || ||||| 
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttt---tctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
      | | |        | |||   | || || ||      | ||  ||| |||  | |||| || ||   |    ||  | ||   |  || ||| ||   ||||| || ||||| || || || ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
------tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
-ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
 |||| ||   | |      | || ||||  |  | ||  ||    | || | ||   || |||| |  ||  |    |  ||  |||    |      |||||| |||||||| || || || ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
tttcatgtatgttttttt-tgcac-ccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattag-ctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
|||| ||    ||       |   |||| ||  | || | ||    | || | ||   || |||| |  ||  |    |  ||  |||    |      |||||| || ||||| || || || ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
ttcatgtatgcatttt--ttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttt---tctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
      ||  | || | | | |     ||   || ||   |  | ||  ||  ||| || |||| || ||   |    ||  | ||   |  || |||  |   ||||| |||||||| || || || || |||||| ||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| 
-----ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgc----tcctaataatt-tttctct-tataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
    |    ||||    | ||| ||  || | ||  || || |  |  |   |||   | | ||   ||  |     |  |  | ||| ||||||| | |    || || || ||||||||||| || ||||||||| ||||||| || ||||||||  ||||||||||||| ||||| ||||||||||||||||| |||||||| 
---gaaagactatt---atggaaacaatgctaatggtaacttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataat--gttctgctcctaataa---tttttctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
 ||   ||  | | |         | || |   || || ||  | || |||   |  || | || |  ||  | ||   ||| |   ||||| |||| |  ||   || ||| | ||||| |  || |||||||||||| || |||||||| | |||||  |||| || ||  | ||||||||||||||||||||| | |||||||  
-tcgtttttttcttc-------ttcattttcactagtacctatatttatattggtggatagttattcagtcttactttgaattacattttttatcttgttgtttgcagTGACTGTGAAACGTACATATCTGCTGATGATCTGAGAATTAATTTATGGAACATGGAGATCAGTGACCAAAGTTTCAATATTGTTGATATTAAGCCTGTC

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgt-tgatattagctcgagttctatactttcat--tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
      | ||| | ||       ||    | | || | |  ||  ||      |    |   || | | ||| | ||   |      ||  | |||||   |||||  | || ||||  || ||||| ||||||||| |||| ||| | |||||||| ||| ||||  |||| |||||||||||||||||  |||| ||  | 
---ctataccttttcagctttgtactccatctcatgtgaagtcttgtgtagctcagcaaacatgttgaagttttactgaaatagcgcttaattttatatgcagCGATTGTGAGACATACATCTCTGCAGATGATTTGAGAATAAATTTATGGAATCTTGAAGTTAGTGATCAGAGTTTCAATATTGTTGACATCAAACCAACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 6
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
                                           || | | | | ||    |       ||||   ||  |  | | | | ||||    || ||  ||||||| | |||||||||||| |||||| |||| ||  | |||||| ||||||||||  | |  |||||||| ||||||||| ||||||| || 
----------------------------------------gtcagctgtttgcattgtggggcgcgtgtctgacgctggtgctctcttttttatg--cagTGATTGCGAAACGTATATTTCTGCTGACGATTTGAGAATCAACTTATGGAATATGGAAATTAGTGACCTTAGTTTCAACATTGTTGATATCAAGCCAGCT

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|163984124|gb|ES173780.1|ES173780
EST:     GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG                         CGACGGCGAAACATTTATTTCNGCTGATGATTTG
genomic: GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGgtaggttatt ... ttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTG
EST: gi|86070772|gb|DR366529.1|DR366529
EST:     GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG                         CGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAA
genomic: GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGgtaggttatt ... ttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAA
EST: gi|86070770|gb|DR366527.1|DR366527
EST:     GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG                         CGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAA
genomic: GTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGgtaggttatt ... ttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
                            tcctaat  putative branch site (score: 2)
                                     tttttctcttat  putative PPT
                               taataatttttctctt  TA-rich tract