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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgctacttacttgctttgtacagccatatgcacatctagatccctctctcacgaattctatacacttgttttatatcctcattaatcatacttgccttaacagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAAGGTGTTCCATCATTAGGGAATCAA

Basic information

species Arabidopsis thaliana
transcript AT3G27470.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0066g00310.t01 (Vitis vinifera), 3'ss of exon 10
gtctgctacttacttgctttgtacagccatatgcacatctagatccctctctcacgaattctatacacttgttttatatcctcattaatcatacttgccttaa-cagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAAGGTGTTCCATCATTAGGGAATCAA
                    || |||  | | |    | |   |  ||  ||||    ||  ||     |  |||| ||  | | |    ||| ||     || |||   || || |||||||| ||||||||||| || || |||||| |||||||| ||||||| ||| | ||||| || 
--------------------gt-cagtgacaagt---tttctctttctaactcaattgtttaatttctcttgtttacattataaatccctatatttcttgaaaacagCCTGCTCATGAGAAAATAGGAGTTGTAGACGCCCAGTGGATTCTACATCAAAGTGTTCCCTCACTTGGGAACCAG

upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S70_58V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------------------------gtctgctacttacttgctttgtacagccatatgcaca-tctagatccctctctcacgaattctatac-acttgttttatatcctcattaatcat--acttgccttaa-------cagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAAGGTGTTCCATCATTAGGGAATCAA-------------------------
                                                                                    || |     ||||  ||     ||    |    || ||| | |     | || |    ||| |   | |||||  |||||     || | |     ||| ||| |       |||   ||||| || ||||||||||||||||||||||| |||||   |||||  | ||| | |||  ||   |                              
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctttctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCGGTTTGTGTTCCTCACAACCATTCAC

upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S70_58V6.2 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------------------------gtctgctacttacttgctttgtacagccatatgcaca-tctagatccctctctcacgaattctatac-acttgttttatatcctcattaatcat--acttgccttaa-------cagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAAGGTGTTCCATCATTAGGGAATCAA
                                                                                    || |     ||||  ||     ||    |    || ||| | |     | || |    ||| |   | |||||  |||||     || | |     ||| ||| |       |||   ||||| || ||||||||||||||||||||||| |||||   |||||  | ||| | |||  ||   |     
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctttctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCG

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|116423910|gb|EG466502.1|EG466502
EST:     ATTTGATTCATGGATGGGGTCTGGACTTTGCCGTTCGGAAATGTGTTCAG                         AACGCCCACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAA
genomic: ATTTGATTCATGGATGGGGTCTGGACTTTGCCGTTCGGAAATGTGTTCAGgtctgctact ... gccttaacagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAA
EST: gi|116423977|gb|EG466569.1|EG466569
EST:     ATTTGATTCATGGATGGGGTCTGGACTTTGCCGTTCGGAAATGTGTTCAG                         AACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAA
genomic: ATTTGATTCATGGATGGGGTCTGGACTTTGCCGTTCGGAAATGTGTTCAGgtctgctact ... gccttaacagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacgaattctatacacttgttttatatcctcattaatcatacttgccttaacagAACGCACACGAGAAAATTGGAGTTGTAGATGCTCAATGGATTATACATCAAGGTGTTCCATCATTAGGGAATCAA
                               cattaat  putative branch site (score: 3)
                                          cttgcctt  putative PPT
                 ttgttttatat  TA-rich tract