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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g64780.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
----gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
    | |  | |||||      || | ||  |      || | | | | |  ||  |  ||| ||||  ||| ||  || ||  ||| || ||||| |  ||||||||| || |||||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || || ||||||
gtcaggaagcatccat---tgcatgtgtttctttt---tttatattttaa--agatagtttgcacaa--gaagttttcttatgtaattattttgtt-gttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 4
---gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
       |  | | |   ||   || ||| |     ||       ||  | |   | |||   || | |||  |  || ||  ||| ||  |||| | |||||||||| || || ||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| || ||||||
gtcaggcagcttcttttgcatgcat-ttctttttttataagtttaat--ttaaatatattttgcagaagaatatttcttatgtaattattctgtt-gtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACTGTGGTCCTTCAG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 4
---gtatacttccatacaca---aatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
   ||    |    |  | |    ||| ||| | ||       | | |   | ||   |  |    ||  ||   | |  |  | | |   || | ||   |||||||||| || || || |||||||| || || || || ||||| || ||| ||||||||||||||||||| ||||| |||||||||||| |||| |||
tcagtgagttattgttgatacttgatagattgacgattttcaaatattggtaccaaggatgt-aaccatttgtcatgatttttttacaatctcctttt---cagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 4
-gtatacttccatacaca---aatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
 ||    |    |  | |    ||| ||| |  |       | | |     ||   |  |   || | |   | |   |  |    | |  ||  ||  |||||||||| || || || |||||||| || || || || ||||| || ||| ||||||||||||| ||||||||||| ||||||||||||  ||| |||
agtgagttattgttgatatttgatagattgacaattttcaaatattggtgacaaggatgt--aaccatttgtcatgattttttttttaaattttcttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCGTTTGGATTTATTACATCAACTGTTACTCTACAG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtatacttccatacacaaata---tattcatgacacattgacactatcatcagccacattggaca-aatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
        | ||  || ||||| ||   | || |||   |  ||    |  | |    |   |       |||| |   ||||       | || ||  ||  |||| |||||||| || || |||||||| || || || || ||||| || |||||||||||||| |||||||||||||| |||||| | ||    ||||||
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctt------tgatttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
-gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttg-----tttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
 | ||| ||     |    || | || || | |  | |     |   | ||| |   |  | || |   || |     | || |||  ||       || ||||| ||||| || || ||||||||||| || || || || |||||||||||| ||||||||||||||||||| ||||| |||||||| ||  | ||||||
agcataattgtgctcc---atgtgtttat-atatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG

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|58665417|gb|CK054103.1|CK054103
EST:     TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
EST: gi|29626495|gb|CB631506.1|CB631506
EST:     GCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: GCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
EST: gi|29683440|gb|CB679715.1|CB679715
EST:     TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
EST: gi|27547116|gb|CA765115.2|CA765115
EST:     TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
EST: gi|29688878|gb|CB685153.1|CB685153
EST:     TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
EST: gi|27920852|gb|CB096660.1|CB096660
EST:     TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAG                         ATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA
genomic: TCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttcc ... tgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG
                       aacttac  putative branch site (score: 2)
                                          tcttgttt  putative PPT
                                 ataaaatcat  TA-rich tract