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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_Os05g16824.3
intron # 21
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 62 (downstream exon)
Score: 4

TACTCGACACTGATCTCACCCCAAAGATATCGGACTTTGGACTCGCCAAGCTATATGATGAGAAGAAGACTCATATCAGCACAGCGATTGCCGGCACATTgtaagaacat ... cattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggctgtaacttcaaaacaaaagctaattgtaacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG
                              ttgtaac  putative branch site (score: 4)
                                            tcattttc  putative PPT
                aaaacaaaa  TA-rich tract