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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaacattcttctttcagctttctctatgtgaaacttcaaaaacttttgtactaattttaagattatcttattcag

Basic information

species Arabidopsis thaliana
transcript AT1G55490.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 4
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgt----ctgtgtaacattcttctttca-gctttctctatgtgaaacttcaa--aaacttttgtactaattttaagattat---cttattcag
  | ||  ||||||| || ||||| || ||||| ||||||||||| || ||||| || |||||||| ||||| |||||  | ||| | |||||||| |||||    |  | ||| |  ||| | ||    |||  |    | ||  ||  |      | | | |  |||  |     | |   |||   |||
ATTAGTCCGGCAAGCTGCAGCCAAGACAAATGATTTGGCTGGTGATGGGACAACGACTTCTGTTGTCCTTGCTCAAGGGATGATCACAGAGGGTGTTAAGgtacaccaatataaaagccttgtatcttaattttacagcataaatattttacttggttctgggaacaatcgtggatctgtttactttcccag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 4
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgt--------ctgtgtaacattcttctttcagctttctctat-gtgaaacttcaaaaacttttgtactaattttaagattatcttattcag-----
  | ||  | ||||| ||||| ||||| ||||||||||||||||| || ||||| || || ||||| ||||| |||||  | ||  |||||||||| |||||         | | |||| |  |   ||  | | ||| ||| || |   |||      | |   | ||  |  | |||| |  || |        
ATTGGTCCGCCAAGCTGCTGCTAAAACAAATGACTTGGCTGGTGATGGGACAACCACTTCGGTTGTCCTTGCTCAAGGGATGATTACTGAGGGTGTAAAGgtacacgctagtatataacctcatgtattggggtatctatatcgtcactgttccggccatgtctcaatatctagaggattttgctactttctccag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 3
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaacattcttctttcagctttctctatgtgaaacttcaaaaacttttgtactaattttaagattatcttattcag-------------------------
| | ||||| |||||||||||||| || || |||||||||||||| || || || || || ||||||||||| || ||| |||| || || |||||||||||  |  ||    |  ||||   |     |   ||| | |  | | ||    |||   |  ||||  | | ||   | |  |                         
GTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattatttgttgtcttattggaaatttagtgtcataactaataactacttggttttgttttttg-taatgcaactaggcctcattttatgttaattttcgcag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 4
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaacattcttctttcagctttctctatgtgaaacttcaaaaacttttgtactaattttaagattatcttattcag-------------------------
  | ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||||||||||||||||||  |||| ||||| ||||||||||||||| |    ||     ||  | ||  |  |  ||||    || |    | |     |||  ||| | | | ||  |                            
ATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgtttttgcttaactcttttgtttggtaaacatgaagaa-catagtaatctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 3
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaacattcttctttcagctttctctatgtgaaacttcaaaaacttttgtactaattttaag--attatcttattcag-------------------------------------------------------------
| | || ||||||||  ||||||| ||||| || ||||||||||| ||||| || || ||||| |||||||| |||||  | || || ||||||||||||||   |  | ||  |  ||    |  ||||  ||||   | ||   |   ||      || |  | ||   |||||  | ||                                                               
GTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcatcacccgcctgaatgtcttcttaatgtagtatttgcgatctttcaaagttactcctcagttgttatcgcactcgaatcgaatattcggctcaatctatgaagttgagctaatctggtcaactttcttcacacgtag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 5'ss of exon 3
GCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaacattcttctttcagctttctctatgtgaaacttcaaaaacttttgtactaattttaagattatcttattcag--------------------------------
| | |||||||||||||| ||||| || ||||||||||||||||||||||| || || ||||| ||||| ||||||||  | || |||||||| ||||||||  ||  |   ||||  |       |||||||| |   | |    | ||| |  |  | | | |     | || |                                      
GTTGGTGAGGCAAGCGGCAGCCAAGACGAATGACTTGGCTGGTGACGGTACCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcacttttctcatcatcaaattctctatatttcattcaggagactgtgat--tcactatggctctctcgtgcctgtgaagctactaaggtttttgcataattctgtag

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|47830371|gb|CK120055.1|CK120055
EST:     CAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAG                         GTGGTAGCTGCTGGTGCAAACCCTGTTTTGATCACCAGAGGTATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaa ... tcttattcagGTGGTAGCTGCTGGTGCAAACCCTGTTTTGATCACCAGAGGTATTGAGAAG
EST: gi|164181589|gb|ES018233.1|ES018233
EST:     ACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAG                         GTGGTAGCTGCTGGTGCAAACCCTGTTTTGATCACCAGAGGTATT
genomic: ACATCTGTTGTTCTTGCACAAGGTTTTATCGCTGAGGGTGTCAAGgtctgtgtaa ... tcttattcagGTGGTAGCTGCTGGTGCAAACCCTGTTTTGATCACCAGAGGTATT