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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagagctcacactactagtgtttctttctctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC

Basic information

species Arabidopsis thaliana
transcript AT1G64740.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
----gtaaagagc-tcacactactagtgtttct---ttctctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
    || ||   | |||     ||    |       || |  |   ||       | |  |        ||  |  || || |||     | ||||| || || || |||||||||||||||||||||||||||||  | |  || || || || |||||||| |||||     | ||||| ||||||||||||
gtacgttaactccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgt--gtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC

upper sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G051782_T01 (Zea mays), 3'ss of exon 4
-------------------gtaaag--agctcacactactagtgtt--tctttctctcttaagtctccttc-tactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
                      |||  |  ||| | ||    |  |  |||| | ||   |||    || |     |||    |    |  |  |   | | |     |||||||| ||||| |||||||| |||||||||||||| || ||  | || || || || || |||||||| ||||| |||||||| || ||||||||||||
gtatatgctcacaactcttaccaagttatatcagattatagattgtaatcttccactgaaaagatagctgcgcgagacatgaatgtctttctctgctgtctcatgcacagGTGCCCTACTGGTTTCAAGTGTGGGATAAACTACCAACCACCAACTGTAGTCCCTGGAGGGGACCTGGCCAAGGTGCAACGAGCAGTCTGCATGATCAGC

upper sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S215_52V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------gtaaagagctcacactactagtgtttctttctctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
                                                     |  |  ||   |  | |    | |    |   |  |    |  || | || || |   | || | |   ||  || |     |||||| |||||||| |||||||||||||| ||||||||||| ||  |||| || || || ||||| || || ||||| ||||| ||||| ||||||||||||
gtaagcagagtggtggtttcagtggtgttgttttagatggtggagtggtgagttggatggcaggcggtgcggtaggtgtgataggtgctggcgcatctccgacaacgc-cgttaactgtggagttctgatgtgtgtagGTGTCCAACTGGTTTCAAGTGCGGGATTAACTACCAGCCACCAACCGTGGTGCCCGGCGGTGATCTTGCCAAGGTCCAACGGGCGGTGTGCATGATCAGC

upper sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ09935 (Selaginella moellendorffii), 3'ss of exon 4
gtaaagagctcacactactagtgtttctttctctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
         | |  || | |  | |||  | | |  |   | ||  || |    || |||    ||  |  |            ||||| || |||||||||||||| || |||||||||||||||||  | |  ||||||   || || ||||| |  ||  | || || || || |||||||||
--------gtaaggct-ccaaagcttcgct-tttgctggctttcaatcgatctaacttttttgctcactacttcca--------agGTGTCCGACTGGATTCAAGTGTGGCATAAACTACCAGCCGCCGACGGCGGTTCCAAACGGAGATCTGGCGAGAGTGAAGCGCGCAGTGTGTATGATCAGC

upper sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ23680 (Selaginella moellendorffii), 3'ss of exon 4
gtaaagagctcacactactagtgtttctttctctcttaagtctcc-ttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
                           |    |||  |||  ||  || | | |   || | |  | |||| |||  |       ||||| || |||||||||||||| || |||||||||||||||||  | |  ||||||   || || ||||| |  ||  | || || || || |||||||||
--------------------------gtaaggctccaaagcttcggttttgcaatcgatctaacttttttgctcac-tacttccaagGTGTCCGACTGGATTCAAGTGTGGCATAAACTACCAGCCGCCGACGGCGGTTCCAAACGGAGATCTGGCGAGAGTGAAGCGCGCAGTGTGTATGATCAGC

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|164105931|gb|ES159042.1|ES159042
EST:     GCCAAACGAACAATTCAGTTTGTTGACTG                         GTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGT
genomic: GCCAAACGAACAATTCAGTTTGTTGACTGgtaaagagct ... ttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC
                                        tcatgttaaaatta  TA-rich tract