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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagtgcttattaccctgtttagcttgtagttattttaaaatgccatggcttttaccaattcataacgaacaatcaacaatctttgtttttcttttcagTATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGGTATGTGTGATGTAGGCATTAG

Basic information

species Oryza sativa
transcript LOC_Os09g28570.3
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 14
actagtgcttattac--cctgtttagcttgtagt-----tattttaaaatgccatggcttttaccaattcataacgaacaatcaacaatctttgtttttcttttcagTATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGGTATGTGTGATGTAGGCATTAG
| ||    |  ||||  || ||||   ||||| |     | | || | ||||||| |||| ||||  |  || |  || |||    ||      ||  | ||||||||||||||||||| |||| |||||||||  ||||||||||||||||||||| |||||||| ||||||||||||||||||                      
attatatttggttacatccggttttcattgtaataggtttttattgacatgccatagcttatacc--tgaattaataaaaattggtaac-----ttcctattttcagTATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG----------------------

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G479068_T01 (Zea mays), 3'ss of exon 2
actagtgcttattaccctgtttagcttgtagttattttaaaatgccatggcttttacca----attcataacg-aacaatcaacaatctttgtttttcttttcagTATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGGTATGTGTGATGTAGGCATTAG
 || ||| |    |   |    |     || || | | |  || |  |   || || ||    ||   | ||       | || ||| ||| | | | || ||||||||||||||||   ||||||||||||| ||| ||||||||| |||| || ||||||||||  |||||||| ||||||                      
-cttgtgttggaaag--taggcactaaataatt-tatcaggatactgtacattgtagcagaaaatatgtcacatggtggtgaataatgttt-tgtatgttctcagTATCAAGGAGAGGGAGGATGGAAGCCACAGAATTACACTGGATTATGCGAGAAGATTCTTGGGAAAAGTCAGACTGTG----------------------
















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|58684560|gb|CK073247.1|CK073247
EST:     ATGCACTTGCAGTCCATGGACGCCTTATTGTAATTGGTATGATCTCCCAG                         TATCAAGGAGAGCATGGATGGAAGC
genomic: ATGCACTTGCAGTCCATGGACGCCTTATTGTAATTGGTATGATCTCCCAGgtatggttga ... ttcttttcagTATCAAGGAGAGCATGGATGGAAGC
EST: gi|33678828|gb|CF307067.1|CF307067
EST:     TGTAATTGGTATGATCTCCCAG                         TATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGAT
genomic: TGTAATTGGTATGATCTCCCAGgtatggttga ... ttcttttcagTATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggcttttaccaattcataacgaacaatcaacaatctttgtttttcttttcagTATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGGTATGTGTGATGTAGGCATTAG
                tcataac  putative branch site (score: 2)
                                    tctttgtttttctttt  putative PPT
                                      tttgtttttctttt  TA-rich tract