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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacatttttatcatctctgttcttgtggctgtaacttcaaaacaaaagctaattgtaacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG

Basic information

species Oryza sativa
transcript LOC_Os05g16824.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g16824.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
-----gtaagaacatttttatcatctctgttcttgtggctgtaacttcaaaacaaa-agctaattg----taacttgtctgtc--------attttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG
       ||   | ||| |   ||   ||  |||||   ||| ||   |||||    | || ||||     ||||      |         |||||| ||||||||||| ||||| |||||||||||| | || |   |||| |||||||||||||| ||    || || || || || || ||||   |   |||  | 
gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA

upper sequence: LOC_Os05g16824.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv10s0092g00710.t01 (Vitis vinifera), 3'ss of exon 22
----gtaagaacatttttatc--atctctgttcttgtggctgtaacttcaaaacaaaagctaattg------------taacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG
     |  |||  |||    |  ||   ||   ||||  || |||   || | |  || |||||||              | || | ||| |  ||| ||||||||||||||||| |||||||||||| | || | | |||| || |||||||||||||||| ||| || || || || || ||||   |    ||  | 
atttctttgaatttttaggccttattgttgaatttgtacctataataacatatcttaatctaattgacctccactaagcgaattttatgtaaaattccagTGGCTATCTGGCACCAGAGTATGCAATGCGCGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGTGTAGTGGCTCTAGAGATCCTCAGCGGGAGA

upper sequence: LOC_Os05g16824.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
------------gtaagaacatttttatcatctctgttcttgtggc--tgtaacttcaa--aacaaaagctaatt--gtaacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG
             |     | || || |    | ||| | | |       || |||||   |    |     | |  |  | || | ||| |  ||| ||||||||||||||||| |||||||||||| | || | | |||| || |||||||||||||||| ||| || || || || || ||||   |   |||  | 
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA

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|25777844|gb|CA752594.1|CA752594
EST:     TATAT-ATGAGAAGAAG-CTTCAT-TCAGC-CAGCGATTG-CGGCACATT                         TGGCTATCTGGCACCCGAGTATNCAATGAGAGGTCGTTTG-CTGAAAAGG-
genomic: TATATGATGAGAAGAAGAC-TCATATCAGCACAGCGATTGCCGGCACATTgtaagaacat ... cattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGC
EST: gi|29627081|gb|CB632092.1|CB632092
EST:     CTATATGATGAGAAGAAGACTCATATCAGCACAGCGATTGCCGGCACATT                         TGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGC
genomic: CTATATGATGAGAAGAAGACTCATATCAGCACAGCGATTGCCGGCACATTgtaagaacat ... cattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggctgtaacttcaaaacaaaagctaattgtaacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG
                              ttgtaac  putative branch site (score: 2)
                                            tcattttc  putative PPT
                aaaacaaaa  TA-rich tract