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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA

Basic information

species Arabidopsis thaliana
transcript AT5G27700.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G134109_T01 (Zea mays), 3'ss of exon 2
gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttga--ctgaatattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA
                    | | |||| | |  | |||  |||      |  |  |  ||     | | ||  || |  | ||||  | ||||   |   |  | |||| || || || ||  || | |||||  ||||||||||||||||||| ||| |||||||||| || || ||||| |||||| |||||   || || ||||| 
-------------------gtacgtttgctgtactttcttgtttaaacctttgccct--ctgc---atggttaattatgttgtgttaatattgagtttctgttcttgcagCTCGGCCACGAATAGGATCATCACTGCCAAGGATCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACC

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G831474_T01 (Zea mays), 3'ss of exon 1
gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA-
            |  | | |     ||||||    || ||   | ||     |  |||| || |             |||| |   | ||  |  |   |  | |||| |  || || ||| |  | |||||  ||||||||||||||||||| ||| |||||||||| || || ||||| |||||| |||||   |  || |||||  
----------gtacgtttgccatacttgtttaaacctttgccctctgca---tggttaattatg-------------ttgtgttaatattgagtttttgttcttgcagCTTGGCCACGAACAGAATCATCACTGCCAAGGATCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGT-CACTTCACCA

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G157300_T01 (Zea mays), 3'ss of exon 1
gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattgg--cagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA
                        | |||||   ||    | ||||         |   ||  |  | | |||||| |||| || |    |||| |  || ||    ||| || || || ||| || | |||||  ||||||| ||||||||||| ||| |||||||||| || || ||||| |||||||||||    || || ||||||
-----------------------gtatgtttgcctcatcctcttgtagaaatatttctgctctgc-atggttggtttttgtgtgctaaggttgagtttatgttctttcagCTCGGCCACAAACAGGATCATCACTGCCAAGGACCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCTTGTATGATGGTCACTTCACA

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G125300_T02 (Zea mays), 3'ss of exon 2
gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattgg--cagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA
                    | | ||||  |    ||||  |     |  |     |    | |    | || |||   || || |    |||| |  || ||    ||| || || || ||| || | |||||  ||||||| ||||||||||| ||| |||||||||| || || ||||| |||||| ||||    || || ||||||
-------------------gtacgtttgcctcatcctcttgtagaaatatttctgctctgcatggttggttttgtt---gtgtgctaaggttgagtttatgttctttcagCTCGGCCACAAACAGGATCATCACTGCCAAGGACCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTATGATGGTCACTTCACA

upper sequence: AT5G27700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S372_10V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatgagaatcatttcttcttcttttgttttggtctctgttttgtgttctctcattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA
       |  |  ||| |  | ||    |||| |    |   ||   || |   |||   |         ||  || | || | ||| |||    |   | || |||||||| | || ||| |||||||||| |||||||||  |||||| |||||||||||  | |||||| | || |  |||||  | |||||||| |||||||| 
--cgcacggtttgttt-tgatgctgcaattttaggggttaactttaattgtggtatttttttttt-----ttttttttggtgtttttttttcttttttctttttgcagTTCTTCAACCAACAGGTTGATCACTTCCAAGGATGTTGCCTCAGTTCAGCTCAATGTGGGTCATGTTGACGAAAATGGTGTCTACACCGGGCAGTTCACC

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaactaagagaagattggttcttgtttgtttgttttgactgaatattggcagTTCTGCTACTAACCGGTTGATCACATCCAAGGATCATGCCTCTGTTCAGCTCAACATTGGTCATTTAGATGCTAATGGCTTGTACACCGGACAGTTCACA
                               tttgtttt  TA-rich tract