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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacctgctttttcaggcaaatccctttatcacatccagttatgttaattttcggaggcatctctagcatgtctgtcataataaacttgtatctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA

Basic information

species Oryza sativa
transcript LOC_Os12g10784.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 7
--ttacctgctt----tttcaggcaaatccctttatcacatccagttatgttaattttcggaggcatctctagcatgtctgtcataataaacttgtatctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA
   | |||| ||     || | |  |||   |||| || ||  | || ||||| |||||  |     ||  |   ||  ||||| | | ||| | ||  | ||||||||||||  |||||| |||||||| | || |||||||| |||| |||||| ||||||||||||||||| ||||||||||||||||
atattcctggttaaggcttgaagataattattttaccagatttacttgtgttacttttctta-----ctgca-tgtgcttgtcaaagtgaacatttacatctccagGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA

upper sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ32189 (Selaginella moellendorffii), 3'ss of exon 5
ttacctgctttttcaggcaaatccctttatcacatccagttatgttaattttcggaggcatctctagcatgtctgtcataataaacttgtatctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA
              | | |       ||||||| |       ||||  | |   | |   | |||  |  || ||           |||| | | || |||| ||| |||| || || |  || ||||| ||||||||||||| ||| || |||||||||||||| |||||||||||||||||||
------------gtaagaagcctttcttatcacct-------tgtt--tctcatgtgttctttcttacgcgtttgc--------gtttgtttgtctctagGTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACA
















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|157651751|gb|EX451385.1|EX451385
EST:     AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCT                         GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTT
genomic: AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCTgtaagttgta ... atctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTT
EST: gi|58681266|gb|CK069953.1|CK069953
EST:     AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCT                         GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGG
genomic: AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCTgtaagttgta ... atctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGG
EST: gi|33681873|gb|CF310112.1|CF310112
EST:     GACAGGAAAAATTATCAACATCAAGAAAGGGACAATTCTGTGCTCCTTCT                         GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTT
genomic: GACTGGAAAAATTATCAACATCAAGAAAGG-ACAATTCTGTGCTCCTTCTgtaagttgta ... atctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTT
EST: gi|58589242|gb|CF987550.1|CF987550
EST:     AGACTGGACAAATTATCAACATCAAGAAAGGACACTTCTGTGCTCCTTCT                         GTTATGGCCAACTCTGCAGAGAAAAT
genomic: AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCTgtaagttgta ... atctttccagGTTATGGCCAACTCTGCAGAGAAAAT
EST: gi|41883464|gb|BX928437.1|BX928437
EST:     AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCT                         GTTATGGTCAACTCTGCAGAAAAAATCAGACTTGCTGGAAATCAAAATGTT
genomic: AGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCTgtaagttgta ... atctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttcggaggcatctctagcatgtctgtcataataaacttgtatctttccagGTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACA
 tgttaat  putative branch site (score: 3)
                                            tatctttcc  putative PPT
                                ataataaacttgtat  TA-rich tract