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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttaaataatcgcaggtgcctctttggtgcgtgtgcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
gtttgttaaa--taatcgcaggtgcctctttggtgcgtgtgct-tgttcaaatga-aatttaatgtagcatataactctt---cagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA
||| |  |    ||||| | |  |  | |||      |  ||| |  | |  ||| ||  | |  ||   | | | |||     || ||||    ||||| |||||||||||||| || || ||||| ||||| || |||||||||||||||||||| || |||||||| 
gttagggatctctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaa-gtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
-------------------------gtttgttaaataatcgcaggtgcc-tctttggtgcgtgt--gcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA
                            || ||||  ||   | ||    |  |   |   ||     |  ||| | | | |  | |   |  |  |  || | ||| |||| |||||| |||||||||||||||| || || || || ||||| || ||||| || |||||||| || ||||||||||| 
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaac-tggct-tccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------gtttgttaaataatcgcagg--tgcctctttggtgcgtgtgcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA
                     |||||    | || ||| |  ||    | |   |  | ||| |   |||  |   |     || |            ||| ||||||||||||| ||||| || ||||||||||| || || ||||| || ||||||||||| || || || || |||| ||| 
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaa-cgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------gtttgttaaata-atcgcaggtgcctctttggtgcgtgtgcttgtt--caaatgaaatttaatgtagc--atataactctt-cagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA
                                                                                               ||| |||   |   |||  | |   |   || || || |    |     ||  |   |||  | | ||  || |     || ||| |||||||||| || ||||||||||||||||| ||| | || ||||| |||||||||||||| ||||| || || ||||  || 
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT

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|124853083|gb|EH937520.1|EH937520
EST:     TTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTACGTCTCAAGACT
genomic: TTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCT-CGTCTCAAGACT
EST: gi|125291724|gb|EL305809.1|EL305809
EST:     ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAAT
genomic: ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAAT
EST: gi|124904196|gb|EH978276.1|EH978276
EST:     ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGA
genomic: ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGA
EST: gi|124883033|gb|EH961935.1|EH961935
EST:     ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAG
genomic: ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAG
EST: gi|124911900|gb|EH985980.1|EH985980
EST:     ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACT
genomic: ATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACT
EST: gi|125289133|gb|EL303218.1|EL303218
EST:     ACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTC
genomic: ACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTC
EST: gi|125042895|gb|EL115164.1|EL115164
EST:     AAATCAAAGCTCACCCGTGGCACAAG                         ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTC
genomic: AAATCAAAGCTCACCCGTGGCACAAGgtttgttaaa ... aactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggtgcgtgtgcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA
                                         atataac  putative branch site (score: 3)
                                               ctcttc  CT-rich tract
                   ttcaaatgaaatttaa  TA-rich tract