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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatcatctccacagttgttataacaaagttcatgattgtatatgtatattgacattatgattgcatctgcag

Basic information

species Arabidopsis thaliana
transcript AT3G53890.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G056828_T01 (Zea mays), 5'ss of exon 3
-TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatcatctccacagttgt-tataacaaagttcatgattgtatatgtatattgacattatgattgcatctgcag
 |||||| || || ||| | |||||||| ||  | ||||| |||||  | |||  ||  || |||||||| ||||||||||  || |||||||||||||||||  |  | |      | || |   ||| |   | |     |  || ||   | | |   ||||||  |||||          |||||   ||| ||  |     |
GTCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCATGTACGATG-TCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgt--gatagtccaggatgtgatgcctacatgcaactttctactgcaattccatgttattgagttca-aattgttggcac---ctgacacagtgaatggctgaatgg

upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G134109_T01 (Zea mays), 5'ss of exon 3
TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatcatctccacagtt--gttataacaaagttcatgattgtatatgtatattgacattatgattgcatctgcag
|||||| || || ||| | |||||||| ||  | ||||| ||||| || |||  ||| || |||||||| ||||||||||  || |||||||||||||||||  |  | |      | || |   ||| |   | |     |  || ||  ||  | |   ||||||      | |  | |   |||||   ||| ||  |     |
TCATGCCTCTGTCCAGATCAACATTGGCCACTTGGATGCGAATGGCCTGTACGATGGTCACTTCACCACGTTTGCTCTCTCTGGGTTTGTCCGTGCTCAGgt--gatagtccaggatgtgatgcctacatgcaactttctactgcaattccgtgtttattgagttcaca----tgttggcac-ctgacacagtgaatgactgaatgg

upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G15800.1 (Glycine max), 5'ss of exon 3
TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatcatctccacagttgttataacaaagttcatgattgtatatgtatattgacat-tatgattgcatctgcag
 |||||||| |||||| | |||||||| ||| | ||||  |||||  |||||| |||||| ||| |||||||||| |||||||||||  |||||||||||||      || |    | |   | ||  |||||| ||   ||   | ||  |          |  | ||| |   | ||| ||  | | ||||   | | |     
CCATGCTTCGGTTCAGATCAACATTGGGCATGTGGATGAGAATGGCGTCTACAATGGCCATTTCTCCACTTTTGCCCTCTGCGGATTCATCCGTGCTCAGgt------atctattttttttcactttttttatattcggttctggaatttctgccttgtttatttttattattgttttattttagcctctatgcaagtaacccttt

upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G05030.1 (Glycine max), 5'ss of exon 2
TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatc-atctccacagttgttataacaaagttcatgattgtatatgtatattgacattatgattgcatctgcag
 |||||||| |||||| |||||||||| ||| | ||||  |||||  |||||| |||||| ||| ||||||||||||||||||| ||  | ||||||||||| |     |||      |  |  ||| | | |  |  |  | |    ||||| ||      ||  | ||||| | | | | ||| |  ||||   | ||      
CCATGCTTCGGTTCAGGTTAACATTGGGCATGTGGATGAGAATGGCGTCTACAATGGCCATTTCTCCACTTTTGCTCTCTGCGGCTTCATACGTGCTCAGgtctaaatttttttcactttttttttattctgttctggaatttctttcttgtt-tatttttattatttattgttt-tattt-ttgcctctatgcaagtataca---

upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S10_32V6.1 (Physcomitrella patens), 5'ss of exon 2
TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttcca-----ctctgctaattactttataatcatc-tccacagttgttata-acaaagt-tcatgattgtatatgtatatt-gacattatgattgcatctgcag-----------------------------
|   |||||||||||| | ||| | |||||||||||||  || ||  | ||||| |||||||||||||| |||||||| || ||||| |||||||| ||||| |   | |   ||     ||  |||| ||| | |     |||  |  | | |||||||  |||   |  |   |||||       | ||  |   |  | ||    |||                                
TGTCGCTTCAGTTCAGTTGAACGTGGGTCATCTTGATGAGAACGGCGTTTACACAGGCCAATTCACCACATTTGCTCTATGTGGATTCGTCCGTGCACAGgtatactattggacagatctcttcgctatttattgttcttgcatagtttatacttgttatttacatcataccgcaattgtgaggagctgtttaatgcttaggtttttgctgacttaggtcgtaactgaatctttttgacgcag

upper sequence: AT3G53890.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S306_29V6.1 (Physcomitrella patens), 5'ss of exon 2
TCATGCTTCAGTTCAGCTTAACATTGGTCATCTTGATGCTAATGGTCTCTACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaatttccactctgctaattactttataatcatctccacagttgttataacaaagttcatg-attgtatatgtatattgacattatgattgcatctgcag
|   |||||||||||||| ||  | |||||  |||| |  || ||  | || || ||||| ||||||||||||||  | ||||| || ||||||||||||||||||||    | | ||   |  |||  ||   ||  ||||     | |   | |    |||| || ||||  | |||     || |||| |  |  || |   |
TGTCGCTTCAGTTCAGCTGAATGTGGGTCACGTTGACGAGAACGGCGTGTATACCGGCCAGTTCACCACTTTTGCCTTGTGCGGCTTCGTCCGTGCTCAGgtttgtga----caattcctttttttagcttgacattctctctctgatcggctttatgtcgttcttgtattggctttgt-cgcggatattaagcata-atgtatcg

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|86060807|gb|DR356564.1|DR356564
EST:     ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCATGCTCAG                         GGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTCGAA
genomic: ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTCGAA
EST: gi|125205341|gb|EL220295.1|EL220295
EST:     ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACA
genomic: ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACA
EST: gi|164211146|gb|ES109742.1|ES109742
EST:     CACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTC
genomic: CACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTC
EST: gi|164206816|gb|ES043164.1|ES043164
EST:     CAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTCGAA
genomic: CAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTCGAA
EST: gi|164205232|gb|ES192637.1|ES192637
EST:     TGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGG
genomic: TGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGG
EST: gi|86086803|gb|DR382562.1|DR382562
EST:     ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGGACAGGCTTTGGCAGAAGAAGAAGGTCGAA
genomic: ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGACAGGCTCTGGCAGAAGAAGAAGGTCGAA
EST: gi|164089665|gb|ES095053.1|ES095053
EST:     CCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGGAC
genomic: CCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGGAC
EST: gi|164005018|gb|ES073090.1|ES073090
EST:     ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTG
genomic: ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTG
EST: gi|164224113|gb|ES059063.1|ES059063
EST:     ACGCTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAG                         GGAGACGCAGACAGTGGCGTGG
genomic: ACACTGGCCAATTCACCACTTTTGCTCTCTGCGGATTTGTCCGTGCTCAGgtttgtgaat ... gcatctgcagGGAGACGCAGACAGTGGCGTGG