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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccatcatgtgcttgcaaaaccaattgttggctttttaaagttttaagtgagattgcttttgtgatatagtgttttgatattatggtttctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG

Basic information

species Oryza sativa
transcript LOC_Os01g05800.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G110063_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------ttgccat-catgtgcttgcaaaaccaattgttggctttttaaagttttaagtgagat-tgcttttgtgatatagtgtttt---gatattatggtttctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
                                                                            ||  ||   |||  || |   |    |  |    |  |    |  ||     |  | |  |||| ||| ||||| |  |   ||| ||||  ||| |||  |||||||||||||||| ||||||||||||||||| |||||||| || ||||| || ||||||||||||||||| |||
gtttctcgatttttttccttctaaaccatactgactattttattttgtgattggttcctgaatatgaatccctttgtgtaatatttgttttttcctgatggctgatacaatcctccctgccttgcaaaaactgtttttttatgacatagtatcatcatgatcttatattttatctgacagGATGTTTTCCAACATTGGCAACAATACCTGTATGGATTGGTCTTTACCAGGCACTTTCAAATGTAGCAAATGAG

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G839422_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------ttgccatcatgtgcttgcaaaaccaattgttggctttttaaagttttaagtgagat---------tgcttttgtgata-tagtgttttgatattatggtttctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
                                                             | |  ||| | | | ||  | |    || ||    |  || |||  |   ||  ||         ||||||| ||| | ||   |  |||  | ||  ||| |||  |||||||||||||||| || |||||||| ||||| |||||||| || ||||| |||||||||||||||||||| |||
gtttcttgaatttttccgtcctaaaccatactgactatttattttgtgcttcattcccgaataggaatccttt-cgtgtgatatttgttttttttctgatatagtactccctgctatgcaataccgtgcttttatgacagtacaatcatgacctcatactttatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAG

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 4
ttgccatcatgtgcttgcaaaacca-attg--ttggctttttaaagttttaagtgagattgcttttgtgatatagtgttttgatattatggtttctcttc---cagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
      | |  |  | |||| | || |||   |||| || |  |  || |      |        | |  | |    ||    | |  ||   ||  ||     ||| ||||| |||||| |||| ||||| || ||||||||||| |||||||||||  | |||||||| ||||| |||
------ttaattattagcaatatcatattagtttggattgtacatattctgttcatgtactgacatatagtctcaacttcaactgtgctgtcatcaatttgtatagGTTGTTTACCAACTCTGGCTACAATTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 4
---ttgccatcatgtgcttgcaaaaccaattgttggctttttaaagtt-ttaagtgagat-tgcttttgtgatatagtgttttgatattatggtttctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
   ||   | ||      ||  |     ||| |   | | ||  | |  |  | ||| || |  | | |   | || |||  ||  || |       | ||  ||| ||||| ||||||||||| ||||| || ||||||||||| |||||||||||  | |||||||| ||||| |||
taattattagcaatattatgttagtttgattttgtacatattctattcatctactgacatatagtctcgacttctactgtactgtcatcaa-----tttttatagGTTGTTTACCAACTTTGGCTACAATTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 4
ttgccatcatgtgcttgcaaaaccaattgttggctttttaaagttttaagtgagattgcttttgtgatatagtgttttgatattatggtttctcttc-----cagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
 | |  |||| |   | ||   |  |||    |  ||   |  |  ||||  |  ||  | |  || |   |    |  | ||  |  ||| ||        |||||||||| ||||||||||| |||||||| |||||||| ||  | || ||||| ||||||||||| ||||| |||
-tactgtcatctttctcca--tcttatttaatgtattcccatttgctaag-aatgttattatgttgttgatgcacatcaacatc-taatttgtccatgtgaacagGATGTTTCCCAACTTTGGCCACAATACCAGTCTGGATAGGTTTGTATCAAGCTCTTTCAAATGTGGCAAATGAG

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|29615536|gb|CB620548.1|CB620548
EST:     GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAG                         GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
genomic: GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgtcgcttact ... tctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
EST: gi|13896049|gb|AU182385.1|AU182385
EST:     GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAG                         GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
genomic: GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgtcgcttact ... tctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
EST: gi|29620327|gb|CB625339.1|CB625339
EST:     GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAG                         GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
genomic: GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgtcgcttact ... tctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
EST: gi|58694651|gb|CK083338.1|CK083338
EST:     GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAG                         GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG
genomic: GCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgtcgcttact ... tctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtgagattgcttttgtgatatagtgttttgatattatggtttctcttccagGATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG
                             ttttgat  putative branch site (score: 4)
                                           tttctcttcc  putative PPT
                           tgttttgatattat  TA-rich tract