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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatcatctaatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacag

Basic information

species Arabidopsis thaliana
transcript AT5G28900.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 11
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatcatctaatttaccttgctact-tcttcacaccaccacatgcgtcttataacatttctaat-gtcaaacggaaacag
| | ||| | |  || ||||| || ||  | |||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||||||||| |||||  | |  |  |   || || |    |  |     |||    | ||       ||||||  |   ||  ||         |||
CTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgatcacaactt--cttgccataaagcagtgaattcactgtta-atcatctaaataacaagttggatcatctttttatttcag

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatcatc--taatttaccttgctacttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacag
| | ||| | |  || ||||| |||||| | ||||| || || || ||||||||||| || |||||||||||||| || ||||||||||||||||| |||||  | || |||  ||||  || ||     | || |  |  |  |     ||   ||||  |  |||||||  ||  | |    
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatccttaataaactttagatttgctgccaagtattaa----gttaaataat-tggctaatgtttaattgtag---

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S68_31V6.2 (Physcomitrella patens), 5'ss of exon 11
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgta---ctaatcatctaatttaccttgctac---------ttcttcacaccaccacatgcgtcttataa--catttc---taatgtcaaacg----gaaacag-------------------------------------------------------------------------------------
  ||||   ||  || || ||||||||| | |||||||| || ||||||||||| |||||  |||||||||||||| ||||||| ||  | ||  |   ||||   | | |||   |       || |  |         ||   || | | |  ||||   |||  ||  ||| ||   || | |||||||    ||  ||                                                                                      
TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatatctcagcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S7_163V6.2 (Physcomitrella patens), 5'ss of exon 11
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtacta-atcatctaattta---ccttgcta-cttcttcacaccaccacatgcgtcttataacatttctaatgtcaaacggaaacag-------------
| | ||  | |  ||  | ||||||||| ||||||| ||||| ||||| |||||||||||  | || ||||| || || ||||| ||||| |||||||||||| ||  |  ||  |||||   | |    | |||  |||           |  |  ||| |||     ||   || | |   ||               
CTTAAAGCGATGCAAATTATCTGGAAACTTCTTCAATATCCTTTTTAACCTCAACAAATTCGTAGCTTTTGAGACTCGTGATCCTTTCCTTATTCGTCAGgtaatatgttctcacatttaagacttcaacatcttaatcagttagttctgagaatgatatcacagcgtgaagaacagatgttcacctaggttggtcatag

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|124943855|gb|EL020008.1|EL020008
EST:     TCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAG                         GAGCGAGAGAACCCTACATTGA
genomic: TCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgtactaatca ... acggaaacagGAGCGAGAGAACCCTACATTGA