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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA

Basic information

species Arabidopsis thaliana
transcript AT2G42810.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
gtaagttctctaaaactttgttgtaataattctt-tgatgttcatgttttaattgcttttgcta--tcactggcaag--gattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaa----atcgccatt-tacacacctttg-tactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
          |||    | ||| | ||| || |  |||  |  || ||   ||    | || ||  | ||| ||      |||| ||||||  |||   | | || |   ||    |||   || |   |||||     |  || || |||| |||||   |  | |||  || || || || |||||||||||||| |||||||||||||| || || |||||||||||||| || ||  |||| |||||| | |||  |||  | ||
---------gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattatt--ctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 7
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
                                                    | |||  ||  |  ||||      |||  |||  |  |  |     ||||| || || |||    ||||| |  ||   | |     |  |   ||  |  | |||| || || || || |||||||| |||||||||||||||||||||||||| ||||| |||||||| || ||  |||| ||| || |||| || || || ||
----------------------------------------------------tacttgagcagtt-ctggtg----ttatgttaacttttgataaaacatgggcttgaa-gttgtagttttactaatattgcactggcaaatctttttaattttccagCTATGTACCTTGCAAGAGGAAATCATGAAAGCAAGAGCATGAACAAAATATATGGCTTTGAGGGGGAAGTGAGGTCAAAGCTGGGTGAGAAGTTTGTTGA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 8
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA-
                                     | ||| |  || | ||  | | | | ||  ||     ||  |   |||||  | ||||||  |||                    ||||||| | |   |||     | | ||   | ||||||||||| ||||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || || ||||||| ||||| ||| || || 
-------------------------------------tcttctttcttcactttatctggttctc-ttgtttgagagaatgctatttgtttttgtct--tggcac-----------------attgtaacttgt--tttgttgccatgtgattttcagcCATATATTTAGCCAGAGGAAATCATGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGAA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
                                                    | ||| |    |||||        ||   || |||   |   | | ||  | ||     | |||   |  ||||||| |     |||     | | ||   | ||||||||||| ||||||||||||| ||||| || |||||||||||||| || |||||||||||||||||||| || || ||||||| ||||| ||| || ||
----------------------------------------------------ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttt----tctcctagtatattgtaacttat--tttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 2
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
                                              |||  || || || || |   |         ||| | |   | |     || ||    ||   |  |  ||| |    |||  |  |   || | | |   ||      |||| ||||||||  | |||||||| || || ||||||||||||||||| || ||||||||||| || |||||  | |||||||||||||||| ||| |||||
----------------------------------------------tttgtttcctcttcctttgtttcatgctctctaagtaacaaaatcacaactaattttattctcatgtaacatct----tgttgactg--gttcaaaaaatctt------cagCTATATATCTCTCTAGAGGAAATCACGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAAGGGGAGGTCAGATCCAAGTTGAGTGAAACATTTGTGGA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
                                       |  ||||| | ||    ||    |         ||||    | |  | ||  ||  || |              || | ||    | |||  | |  ||||   |   |   | |   ||  | || ||  | ||||| || |||||||||||||||||||||||||| ||||||||||| || ||||||    | ||||| | ||| | | |     |
---------------------------------------tatatgttctgatgagcttattcagtgtatatcagga---gactgatcacacttaactca-------------ctctacttcctctctaa-cctcgttttatttattgtctgaatagGGC--TGTACCTTTCTAGAGGTAATCATGAAAGCAAGAGCATGAACAAAATATATGGTTTTGAAGGGGAGGTTAACGCGAAGTTCAATGAGACAATGAATAA

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgt-----actg--cagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
                                                               | | | |  | || |   || |||  |  |   | | | |  | |    |  || |||  || ||    |||  | |||    |||||     | ||   ||   | || ||  ||||||| || |||||||| ||||||||||||||||| ||||||||||| || || ||     | ||||| | ||| |   |   | |
-------------------------------------------------------------agtaagttgtgatgagtttgttgttt--ttgtaaatcaggagactgagtcctgtcaatttttttataccctgcc--taacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA

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|124933978|gb|EL011087.1|EL011087
EST:     CACTTTGTTTGCTTTCAAGTGCATGTGCCCATCAT                         CCATATATCTAGCCAGAGGAAACCATGAAAGACAAGAGCATGAACAAAATT
genomic: CACTTTGTTTGCTTTCAAGTGCATGTGCCCATCATgtaagttctc ... tgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAG-CAAGAGCATGAACAAAATT
EST: gi|125303143|gb|EL317228.1|EL317228
EST:     CGTTGAGATCATCCTCACTTTGTTTGCTTTCAAGTGCATGTGCCCATCAT                         CCATATATCTAGCCAGAGGAAACCA
genomic: CGTTGAGATCATCCTCACTTTGTTTGCTTTCAAGTGCATGTGCCCATCATgtaagttctc ... tgtactgcagCCATATATCTAGCCAGAGGAAACCA
EST: gi|125194335|gb|EL209289.1|EL209289
EST:     CGTTGAGATCATCCTCACTTTGTTTGCTTTCAAGTGCATGTGCCCATCAT                         CCATATATCTAGCCAGAGGAAACCA
genomic: CGTTGAGATCATCCTCACTTTGTTTGCTTTCAAGTGCATGTGCCCATCATgtaagttctc ... tgtactgcagCCATATATCTAGCCAGAGGAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaaagtttccattttaattgtaaatcgccatttacacacctttgtactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
              ttttaat  putative branch site (score: 3)
                                       caccttt  putative PPT
             attttaattgtaaat  TA-rich tract