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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccttttaaattacatttatataactttatataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG

Basic information

species Arabidopsis thaliana
transcript AT4G37750.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
---------------------gtccttttaaattacatttatataactttatataatacatagtt-taataatgtgaatattgactttgtgtga-gttttttgtact--agACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                        | | |  |||    ||  |||| | | |  |  ||| | |   |  ||  |  |   | ||| |||   | |||   || | |  || ||||||||||||||||| |||||||| |||||||| || || ||||| ||||| ||  | || || || |||||  
gtgtttcattttgtgctgaacaagcatatgcatttttcttg-ataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 6
---------------------gtccttttaaattacatttatataactttatataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtact--agACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                     | |     |  |  | |   ||| | | |    |  ||  |  | | | | | ||   |   |  ||     | |   || | |  || || |||||||| ||||| |||||  | |||||||| ||||||||||||||||| ||||| ||||| || |||||  
gttcgtctgtgcagggattgcgccaccgcatctcgcttccttattattgtgcggacaactaacgtaagtgaagagatcgtct-caatgcacacgctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G063994_T01 (Zea mays), 3'ss of exon 3
gtccttttaaattacatttatataactttatataatac-atagtttaataatgtgaatattgactt--tgtgtgagttttttgtact--agACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG----------
            | | |||    |   |  |||   ||   | |||  |    |  | || | ||   |||    | |   || | |  || || |||||||| ||||| |||||  | |||||||| || |||||||||||||| ||||| ||||| |  ||||||           
-----------gttcgtttgcccagactactatgccaccgcattttgcttccttagagatcgtctcaatgtacacgctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGGGTCGCTGGAAACAAGGATCTATACCTCGACACTTTTAGTAAGAAAGA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
--------------------------------gtccttttaaattacatttatataactttatataatacat-agtttaataatgtgaatattgactttgtgtgagtt--ttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                                 | |  ||  ||||    ||||  | | | | | |||  | |   | | | |   ||  ||   |     |  |||  |||  ||  ||||| ||||| ||||||||||||||||| || ||||||||||| ||||||||||||||||| || |||||||| ||  
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 9
--------------------gtcctttta-aattaca-tttatataactttata-taatacata-gtttaataatgtgaatattga--ctttgtgtgagtt------ttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                     ||  | || ||||||| ||||  ||    |||| |||||  ||  | |   ||||  | |  | |   ||| |   | ||      ||| |||  ||||| ||||| ||||||||||||||||| || ||||||||||| ||||||||||||||||| || |||||||| ||| 
gtctcataggccaacaaccactcagtatataattacaatttaattagtaatatactaatatttatatctgcaaatgaaatttctaaagttttttcaaacttggttcatttggtagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTTA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 7
----------------------------------gtccttttaaattac--atttatataactttatataa---tacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                                    |  ||||| |||   || | || | ||| | |  |   ||| | |||  | | |  |   ||| | | ||  | |    || |||  || || ||||| || |||||||||||||| || ||||| ||||| ||||||||||||||||| || |||||||| ||  
gtctcacaggctagcatttacacagtatatgcattgcaatttaatttaacaatatttacaccttgagaagaatttactttgttctaaactcggttcattcattctgattaa---cttggtagCAGGCACCACCAACACGGAAGGTGGCAAGCTCGAATTGGAAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
----gtccttttaaattacatttat-ataactttatataatacatagtttaataatgtgaatattgactttgt----------gtgagtttt--------ttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
    |   ||  | | || ||  ||  ||| || || ||| |     |  |   |    |  ||| |||||||          ||   || |        | |||  || || ||||| ||||||||||||||||| || ||||| || || || |||||||||||||| || |||||||| ||| 
gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaattaactttgttctaaactcagttgattctgattaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 6
gtccttttaaattacatttatataactttatataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                      |||     |    || ||  ||      || || |  | ||    | | | |  |       ||||| || || || ||| | |||||||| |||||||| ||||| || || ||||||||||| ||||| ||||||||  
---------------------gtaagc--gtgccgtaaatccttctcctttgcgattcctaacaagctttaaatcatgc-----agACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA

upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 6
gtccttttaaattacatttatataactttatataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                      |||     |    |  ||  ||  |    | || |  | ||    | | | |  |       ||||| || || || ||| | |||||||| |||||||| ||||| || || ||||||||||| ||||| ||||||||  
---------------------gtaagc--gtggcgtgaatccttctacttcgcgattcctaacaagctttaaatcatgc-----agACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
                         tattgac  putative branch site (score: 2)
                                          ttttttgt  putative PPT
       atagtttaataatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttttaaattacatttatataactttatataatacatagtttaataatgtgaatattgactttgtgtgagttttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA