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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttaaaatcatcgtttaaacagaacctaaaagattctgtgttgtgataaaactttgtggaattctatgatcagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA

Basic information

species Arabidopsis thaliana
transcript AT4G27180.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 15
--------------gtaagcatttaaaatcatcgtttaaacagaacctaaaagattctg--tgttgtgataaaactttgtggaattctatgat----cagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA
                |     || |     || ||         | | || ||||     || | | |||| | | | | |||    ||| |    ||||| ||| ||||||| ||||| ||||| |||||||||||||||||  |||| || ||||| |||   |||||||| || ||||| |||||||||||| |||
cgtttttgaattccacactatattgacgatttctttgttgtttgccttgaatgatttgagatgatctaataataatctcttgaacatgatggttgaacagCCTTGTCTAGGTGGAGACTCCAAGACACTAATGTTTGTGAACATATCACCTGATCCTTCTTCAGTTGGTGAGTCACTATGCTCACTCAGGTTTGCATCAA

upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 16
----------gtaagcatttaaaatcatcgtttaaacagaacctaaaagattctgtgttgt------gataaaactttgtggaattctatgat----cagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA
           ||   | || |     |  |||     |  | | || ||||     |  |        ||| | | | | |||    ||| |    ||||| ||| ||||||| ||||| ||||| |||||||||||||||||  |||| || ||||| ||||  || ||||| || ||||| |||||||||||| |||
gaattccacactacaaaattgatgatttattttttgttggccttgaatgatttgagataatctaataattaataatctcttgaacatgatggttgaacagCCTTGTCTAGGTGGAGACTCTAAGACACTAATGTTTGTGAACATTTCACCTGATCCTTCTTCAATTGGCGAGTCACTATGCTCACTCAGGTTTGCATCAA

upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA12G34330.1 (Glycine max), 3'ss of exon 15
-------------gtaagcatttaaaatcatcgtttaaacagaacctaaaagattctgtgttgtgataa--aactttgtggaattctatgat-----cagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA
              | |  || | || |     |||      | | |  ||   | || | ||   |||      || | |||| | ||| |     ||||| ||| ||||||||||||| |||||  ||||||||||||||||| | || || |   | ||| | || ||||| || ||||| ||  |||||||  |||
cagatttgacaattttactatattaattgcatctttgttgctatcttgtaatcatttgaggtgatctaatttgtgttcttgaatacaatgctgaacacagCCTTGTCTAGGTGGTGACTCAAAGACATTAATGTTTGTGAACATCTCTCCTGACCAAGCTTCAGCTGGAGAGTCACTATGCTCACTACGGTTTGCGTCAA

upper sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 15
---------------gtaagcatttaaaatcatcgtttaa-acagaacctaaaagattctgtgttgtgataaa-actttgtggaa----ttctatgatcagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA
               |||| ||| | |  |  |  | ||| |      | |  | | ||||  ||| | ||   | | |||  ||    ||   | ||||||| ||||||||||| ||||| |||||  | ||||||||||||||| | || || |||||||||   || ||||| || ||||||||  | || ||||| |
tatcagggcccctctgtaa-catgttactttctattctaacattatttccattacaatctgccttgggttacttattatgttcaaatattttgtttatcagCCTTGTTTAGGTGGGGACTCCAAGACCTTGATGTTTGTGAACATCTCTCCTGATCCTTCCTCATTGGGAGAGTCGCTTTGCTCCCTACGTTTCGCAGCCA

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|125209189|gb|EL224143.1|EL224143
EST:     ACTCAAAGCTCACTTATCTTCTTCAG                         CCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCA
genomic: ACTCAAAGCTCACTTATCTTCTTCAGgtaagcattt ... ctatgatcagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCA
EST: gi|116407359|gb|EG449951.1|EG449951
EST:     AAGAAGATCACGTTCCTTTCAGAAACTCAAAGCTCACTTATTTTCTTCAG                         CCCTGTTTAGGTGGTGACTCGAAGACGTTAATGTTTGTGAACATCACCCCA
genomic: AAGAAGATCACGTTCCTTTCAGAAACTCAAAGCTCACTTATCTTCTTCAGgtaagcattt ... ctatgatcagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagaacctaaaagattctgtgttgtgataaaactttgtggaattctatgatcagCCCTGTTTAGGTGGTGACTCGAAGACGCTAATGTTTGTGAACATCACACCAGAACCTTCCTCAACCGGTGAGTCTCTGTGCTCCCTCAGGTTTGCAGCAA
     acctaaa  putative branch site (score: 3)
                           ataaaacttt  TA-rich tract