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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC

Basic information

species Arabidopsis thaliana
transcript AT1G16710.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 9
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
            |    | |  |     |||||   ||||     |||   |  ||||  || ||   ||    ||   | | |  ||  |    || ||    |||  ||||  || ||  |||||||||| ||||||||||||||||| ||| | ||||| |||||||| |||||||||||  | ||||| ||  | || || || || |
------------gtaagaaattagtccagtattc-tttcaaaagaacaccaatcatttcaagcataaatcatacgtgaaactgttttttat----caaat---gtttggcagGCTGTCCTTTTGTTCCAGAAAATAGAAGGTGTAGAAGTGTGCCTATTTGGAATGTATGTTCAAGAATTTGGTGCAGAATGCTCCTACCCGAACCAGCGTC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
-----------------------gtaaga-atgatcgacgcacaccatcattgtatttgct---tcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgt--tcgtgctccacattt-----tatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
                       | || |  |||||| | |      | | |   | |      |  | |||  | | ||  ||||    | |          | ||| ||| |  |  |  |  ||||||     |||||  ||||   ||||  | || ||||| ||||||||||| ||||||||||| ||||| |||||||||||||||| |||  | |||||   |   || || ||||| |
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 2
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgc-tccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
               | |     ||||| |  |   || | |    |||  | | |  |||  | ||     |  || |     |   |||   |  |     | ||   ||||  |||||  |||||||||| ||||||||||| ||||||||  | ||||| |||||||| |||||||||||  | ||||| ||    || || || || |
---------------gtaagaattcattcttgtcatttgaag----catgaattgtagtcacaactcacacgtactaatttctgcaaccgtatatttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAAAATAGAAGGTGTGGAAGTATGTCTATTTGGAATGTATGTTCAAGAATTTGGTGCTGAATGCTCTTTCCCGAACCAGCGTC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
               | |     ||||| |  |   || | |     ||    || || ||         |  || |  | |||  ||  ||    | || ||      ||||  |||||  |||||||||  ||||||||||| ||||||||  | ||||| |||||||| |||||||||||  | ||||| ||    || || || ||||
---------------gtaagaattcattcttgtcatttgaagcatgaatc--gtagttacactcactaatttctgcaacactattttttatg----aaatgttg---gacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
                       | ||   |     || || |    || | ||  |    | ||   |       | || |||  ||  ||| |     ||| | |  ||||| ||| || |||| || |||||||||||||| ||||| ||| | ||||| |||||||| |||||||||||||| ||||||  |  ||| ||||| ||||
----------------------gtgatgagaa--agttgatttatcaatctgatcgtaatcgaatcattaatcatgaatattat--ttgatgcccttagctttctattccagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
                      ||       ||   || ||     |  ||   ||       | || |   |  |   ||||   ||  | | |     ||| | |  ||||| ||| || |||| || | |||||||||||| ||||| ||| | ||||| |||||||| |||||||||||||| ||||||  |  ||| ||||| ||||
-------------------gtgatgggaaagttgattttatccatccgattgtaatc-----aaatcattaatcatg--aatacttttgattcccttagctttctattccagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
    | |||   || | | |  |   |  | |||  |||||    | | || | |     | || |    |  || | | |    | | ||      | ||||  ||  |||||  || || |||| |||||||| ||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||||  |   || |||||||| |
----gtatgcaggatgtatattaagttgatgttt-tttcat----atagttgaca-----aagacttaaattatgaactgaa---gattgt------ctttttcgtttccagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------gtaagaatgatcgacgca--caccatcattgtattt---gcttcatgtccac-atttaatattttcaggattcctctcttgtagtaatatcgttcgt--------gctccacattttatttat-cagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
                  | ||  ||  | ||  |    |||   |||| |||      |||||| ||| || |  |   ||   | || |  | ||    |||     ||  |        | |    |||||  |||| ||||||||  ||||||| || ||||| |||||||||||||| ||  | || || |||||||||||||| |||||    ||||| ||   ||| ||||| ||  
gtatattttgcttgtggtttagtgtggccaacaaagtttccaagcttgtctttcaaaactcatgttcacgatgtttttgctttgtggtttcaatgttaatataagcgtatttatagggacttgtttgctatttttgttattcagGTGGTATTGCTGTTTCAAAAGATCGAAGGTGTAGAAGTTTGTCTCTTCGGCATGTATGTCCAAGAGTTTGGGATGGAATGCTCTCTTCCAAATCAGCGAA

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|116434362|gb|EG476954.1|EG476954
EST:     AAATTTTTCGGGAGGATAATTTTCCGACAGAATTTCCATACAAGTCCAAG                         GTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGG
genomic: AAATTTTTCGGGAGGATAATTTTCCGACAGAATTTCCATACAAGTCCAAGgtaagaatga ... tatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC
                                          ttttattt  CT-rich tract
                                       acattttatttatca  TA-rich tract