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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacaccgacattcaaattttttcgaacacaaatatttaggctaaaggtctttattgttctttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT

Basic information

species Oryza sativa
transcript LOC_Os12g10784.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 6
gtaagttacaccgacattcaaattttt---tcgaacacaaata--tttag-----gctaaaggtctttattgttctttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT
|||||||  |    | |  | || ||     | || |  | ||  ||||      | | |    |  | || | | |  | |||||||||| |||||||||||||||||| |||||||||| ||||| || ||| | || | ||||| |   |||| ||| ||  |    ||   | | | |||  
gtaagtttgatatccttcaatatattcaagccaaatatcagtaaatttaccctttgtttatccccccttttctccatcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA
















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|88258518|gb|CI361104.1|CI361104
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCTCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88505479|gb|CI432985.1|CI432985
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGGGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88253440|gb|CI352066.1|CI352066
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|163925412|gb|EG711549.1|EG711549
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86841827|gb|CI337475.1|CI337475
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|4714258|gb|AU058225.1|AU058225
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88295502|gb|CI527865.1|CI527865
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|12693436|gb|AU173569.1|AU173569
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86603000|gb|CI357364.1|CI357364
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAACCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88836262|gb|CI371367.1|CI371367
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAACCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|11442603|gb|BF430506.1|BF430506
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86833012|gb|CI333611.1|CI333611
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|33672946|gb|CF301185.1|CF301185
EST:     CCATTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|88473662|gb|CI410933.1|CI410933
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86526749|gb|CI166955.1|CI166955
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCGCCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|33688394|gb|CF316633.1|CF316633
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|7404274|gb|AU066118.2|AU066118
EST:     GGCCA-TGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCNAA
genomic: GGCCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
EST: gi|86839037|gb|CI330405.1|CI330405
EST:     CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCT                         CGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA
genomic: CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAA

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: 48 (upstream exon), 73 (downstream exon)
Score: 21

CCACTGCGCAATTTGGAGGAGCTATTAGAGGAGCTGATTGCAATTGCTgtaagttaca ... ttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttcgaacacaaatatttaggctaaaggtctttattgttctttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT
                       ggctaaa  putative branch site (score: 21)
                                tctttattgttctttc  putative PPT
         aacacaaatattta  TA-rich tract