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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTCGTTTACTCTTTCAAAGCTAAGCTTTCAAGATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcag

Basic information

species Arabidopsis thaliana
transcript AT5G27700.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27700.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G15800.1 (Glycine max), 5'ss of exon 2
----GACTCGTTTACTCTTTCAAAGCTAAGCTTTCAAGATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaatcatttcttcttcttttgtt--ttggtctctgttttgtgttctctcattaactaagagaagattggtt-cttgtttgtttgttttgactgaatattggcag---------------------------
             |   || ||  ||| | |    |||||||| ||||| || || ||| ||||||||||||||||||||||||| ||||| || |  | | | || |      ||||  ||  | | |  ||||||     |  ||   | |  || | ||| ||  || ||||||  ||  |  |  || |||| |                            
ATCTTTGCGAAGGAGGTTTACAGCGCTCAACCA--AAGATGCAGAACGAGGAAGGACAGATCACTGAGCTTTACATTCCTAGGAAGTGgta-tgcgctttaatcctgcaatcactgttcgttaatttttaatttgtggggatttttt---ttaatgatggttgtttatttatttgttctttgagtttttattttggaatttgaatggatttgtgaatttggtgcag

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G05030.1 (Glycine max), 5'ss of exon 1
-------------GACTCGTTTA----CTCTTT-CAAAGCTAAGCTTTCAAGATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcag--------------------
             ||    | |     | ||||  ||  || | | |  |||||||| ||||| || || ||| |||| |||||||||||||||||||| ||||| ||||  | | |||| ||     ||||    | | |  ||| ||     |  |    |||  |  | ||  || |||  | ||| ||||   || |  |||   |                    
ATTCAGGTTTATAGATCTCTGTGAAGTCGCTTTATAACACTCAACCT--AAGATGCAGAACGAGGAAGGACAGATCACCGAGCTTTACATTCCTAGGAAGTGgta-tgagctttaattctcctatcactgtt--aatttttagtttttggaaaattttggtttaatggttgtttatttgttgagttttttttttttttggaatttgaatggatttgtgaatttggtgcag

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G05030.2 (Glycine max), 5'ss of exon 2
-------GACTCGTTTA----CTCTTT-CAAAGCTAAGCTTTCAAGATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcag--------------------
       ||    | |     | ||||  ||  || | | |  |||||||| ||||| || || ||| |||| |||||||||||||||||||| ||||| ||||  | | |||| ||     ||||    | | |  ||| ||     |  |    |||  |  | ||  || |||  | ||| ||||   || |  |||   |                    
GTTTATAGATCTCTGTGAAGTCGCTTTATAACACTCAACCT--AAGATGCAGAACGAGGAAGGACAGATCACCGAGCTTTACATTCCTAGGAAGTGgta-tgagctttaattctcctatcactgtt--aatttttagtttttggaaaattttggtttaatggttgtttatttgttgagttttttttttttttggaatttgaatggatttgtgaatttggtgcag

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|116476469|gb|EG519061.1|EG519061
EST:     ATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATG                         TTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCT
genomic: ATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaa ... atattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCT
EST: gi|164031513|gb|ES005094.1|ES005094
EST:     TTCCTAGGAAATG                         TTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCTTCTGTTCAGCT
genomic: TTCCTAGGAAATGgtaatgagaa ... atattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCT
EST: gi|125090732|gb|EL148605.1|EL148605
EST:     ATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATG                         TTCTGCTACTAACCGGTTGATCA
genomic: ATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaa ... atattggcagTTCTGCTACTAACCGGTTGATCA
EST: gi|116433168|gb|EG475760.1|EG475760
EST:     ACGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATG                         TTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCT
genomic: ATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaa ... atattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCT
EST: gi|125186190|gb|EL201144.1|EL201144
EST:     GAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATG                         TTCTGCTACTAACCGGTTGATCACATCCAAGGATC
genomic: GAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaa ... atattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTCGTTTACTCTTTCAAAGCTAAGCTTTCAAGATGCAAAACGAAGAGGGTCAGGTCACTGAGCTTTACATTCCTAGGAAATGgtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcag

- - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT