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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os04g41470.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 7
-----gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
       || | | ||  ||  |   |      |  || | |||||||     ||    | ||  ||||  ||| || |  ||| ||| |   | ||||||||||||| || |||||||||||||||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| |||||||| || |||||||||||||||
ttcctctctctctcttaatgcaaccatgcacagatctcctgtgtttttgagaaaaaaactgtccagtgttgactttgct--actgtctat---tcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
-------gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
         || | | ||  ||  ||| |     || ||| |  || |||   ||||   || ||   | |  |||  |   |||| ||| ||    ||||||||||||| || |||||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| || |||||||||||||||
tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttga-gcaaaa-atatccaatattgacttcg--aaactgtctatt---catggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
-------gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
          ||   ||| || || |     |  |||   |   ||   |  |||   | |  | |||| |      || | |  |   | |||       |||||||||| | || ||||| ||||| ||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| ||||| || ||||| |||||||||
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgc--ttcacattttgttttgttgctgctaagttccatattga-----atttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 7
gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggttt-----cagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
       | || |   | | | |    ||  | | |    |  |||  ||| ||||| |  |    | |    |   |||  |  |  |    ||||     ||||||||| || ||    || || || || || || ||  |||| ||||| |||||||| || || ||||||||||| ||||||||||| ||||||||||||
-----gctattctaaccctctaatctctatatgtaagaagtgaacttgaagatatttgtcttagagaatgacctattcttattcattatcgctgttttaaaacagGATTCTTGCAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
gactttatttttttgtc-atattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggttt-cagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
 | | |   ||   |   |||||    || |   || |  ||  |    || | ||   || |    | | ||||    ||| | |   || |  |   ||||||||| || ||    || || ||||| || || ||  |||| || ||||| || || || |||||||||||||| |||||||| || ||||||||||||
aaatatgcgttcgagctgatatt--ctgtcgacttttttcttagagaataactcatcctttattcatattgtgttcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG

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|29623493|gb|CB628504.1|CB628504
EST:     GTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG                         GATTCTAGCTAATT-AAAGCCTTGTCCT
genomic: GTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTGgtattgtcag ... atggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCT
EST: gi|29681156|gb|CB677431.1|CB677431
EST:     GTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTG                         GATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGNNNN
genomic: GTTTCAAAGTGGATCCTCAAGAACAGTGCGGAGTCTGAAAATATGAACTGgtattgtcag ... atggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG
      ttatttctt  TA-rich tract