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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttaattacaatattctattttattgtaatgggttttcttgttatgtagtttttctatagacttcttgacatcttccttgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCACTATATGCGTAATGTTATTGCCATTGAACCATCATGGCTTACGGAAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g11370.1
intron # 22
splice site 3'
intron type U2

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|29658870|gb|CB655145.1|CB655145
EST:     ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAG                         GGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
genomic: ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAGgtgagtttaa ... tgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
EST: gi|29624814|gb|CB629825.1|CB629825
EST:     ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAG                         GGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
genomic: ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAGgtgagtttaa ... tgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
EST: gi|29667511|gb|CB663786.1|CB663786
EST:     ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAG                         GGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
genomic: ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAGgtgagtttaa ... tgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
EST: gi|29625176|gb|CB630187.1|CB630187
EST:     ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAG                         GGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA
genomic: ATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAGgtgagtttaa ... tgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCA

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: 65 (upstream exon), 59 (downstream exon)
Score: 21

GAATACAGCCAGAATGGGATGTACAAAACAATAAGGACCTCACAAGAAGTTTATATTCATCCTTCTTCTGTGCTATTTAGgtgagtttaa ... tgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCACTATATGCGTAATGTTATTGCCATTGAACCATCATGGCTTACGGAAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttgttatgtagtttttctatagacttcttgacatcttccttgcattttagGGTTAATCCAAAGTGGGTCATCTACCAGTCTCTAGTTTCAACTGATAAGCACTATATGCGTAATGTTATTGCCATTGAACCATCATGGCTTACGGAAGCT
                              tcttgac  putative branch site (score: 21)
                                      tcttccttgcatttt  CT-rich tract
                tttttctata  TA-rich tract