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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

Basic information

species Arabidopsis thaliana
transcript AT4G29900.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
gttcaatac---atttacattcc-tcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccc----cccaacttt-cagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
||| |   |   | | |  |||| || | | |  ||      ||  | ||   | |   |  || |  |  ||| | ||   |    |  |||||   ||||||||||||||||| | ||||| ||||| || || |||||||| ||||| |  || || || || |||||||||||||| |||| ||| || |||| |
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
---------------------------------------------------gttcaatacatttacattcc----tcgtatgtgtaagctttaaaaatacactgttattgaggatc-----acactttctgt----------gttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
                                                   |||    ||||  || |||      |  || |||||  |  | ||  |   |   || || | ||     |||  || |||          |   | |   ||||| ||||||||||| |||||  ||||||| || || || || |||||||| ||||| |  || || || ||||||||||||||||| ||||  || || |||| |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
-----------------------------------------------------------gttcaatac--atttacattcctcgtatgtgtaagctttaaaaata------cactgttattgaggatcacactttctgtgttg---------ccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
                                                            || || |   | || ||     |  || |||||  |  | ||  |      ||| | | || | ||     ||||| ||  |          | |   ||||| ||||||||||| |||||  ||||||| || || || || |||||||| ||||| |  || || || ||||||||||||||||| || | ||| || |||| |
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 24
--gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttc-------agGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
  |||  |   ||          |    || |  | | |||      |   | | |     | |  || | | |||    |   |  |||        |||| ||||||||||| ||||||||||||||||| || |||||||| || || |  || || |||||||| ||||||||||| ||||  || |||||||||
aggtttgaactatcatttcaatgcaggagtttttgttctaatgtagtaaactaactagcttttattctgtttttgtaattctatacattttggaatatagGCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 24
-----gttcaatacatttacattcctcgtatgtgtaagctttaaa--aatacactgttattgaggatcacacttt--ctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
     |||  |   ||          |  |||| |  | | |||   | || |||    || |   |     | |   | | |            |  |||| ||||||||||| ||||||||||||||||| || |||||||| || || |  || || |||||||| ||||||||||| ||||  || |||||||||
taaaggtttgaactatcattccaatgcagatgtttttgttctaatgcagtaaactagcttttattcttttcttgtaattctatacatttttggaatatagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
---------gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttatt--gaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
          |  | |    | |||    |  |  ||  ||  | |   ||     | || ||   | | |     ||       |        | ||| |||| ||||| ||||| ||||||||||||||||| || |||||||| || || |  || || |||||||| ||||||||||| ||||  || |||||||||
tctattagaatctattgttctgacacattttttg-gttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagttt-agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
---gttcaatacatttacattcctcgtatgtgtaagctttaa--aaatacactgttattgaggatcacactt-tctgtgttgccccccaact---ttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
    |  |||  |||       | |  || | |  | |  ||  |  || |||  | ||     |||   || | | |||  | |      |   || |||| ||||| ||||| ||||||||||||||||| || |||||||| || || |  || || |||||||| ||||||||||| ||||  || |||||||||
ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
gttcaatacattt---acattcctcgtatgtgtaagctttaaaaata-------cactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
 |  ||||  |||   | ||   |  |||    ||  |||    |||       | || || ||     |     ||||| | ||        ||||| |||||||||| ||||| |||||||| ||   ||| || || |||||||| || |  || ||||||||||||||||||||||| ||||  || ||||| |||
ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggacttt-agGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 22
gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
                            ||  | |||     ||     | || |  || | || ||||||   ||     |   | |||||| ||||| |||||  ||||||| |||||||| ||||| || || || ||||  |||||||| || ||  ||||||||||||||| ||| ||||| |||
----------------------------gtggg-tttggcggta----atcatcgtaga-cgcattttctga--tgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
                            ||  | |||     ||     | || |  | || || ||||||   ||     |   | |||||| ||||| |||||  ||||||| |||||||| ||||| || || || ||||  |||||||| || ||  ||||||||||||||| ||| ||||| |||
----------------------------gtggg-tttggcggta----atcatcgtag-tcgcattttctga--tgataaactgttatcagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
                                     ttgcccccc  CT-rich tract
           tgttatt  TA-rich tract