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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaatatccttgcccttcttgtttctatatctttggacaatctaattactggtgtaattcaatcttcttttgcaatctttggacttcttttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC

Basic information

species Oryza sativa
transcript LOC_Os08g08220.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08220.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G449355_T02 (Zea mays), 3'ss of exon 8
tgcaaatatccttgcccttcttgtttctatatctttggacaatctaattactggtgtaattcaatcttcttttgcaatctt----tggacttcttttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC
       ||   ||   |||   |||  ||     || |    ||    | || | |  ||    ||| ||||  |    |    || | | |   |   |||||||  ||||||||||||  | ||||| || ||||| ||||| |||||||||||||||||| | || || ||||| ||||||||||||||||| ||  |||
----gcaatagctggttttcaaattttcattctactgcatgcactttaaaatgctttgctttcggcttattttatatgtctgcaatgaattacaccttttgcagGATACACCTGAGGATGCTATTGTGACAATTTGTGGTCATGTTTTCTGCTATCAATGTATACATGAACGAATAACGACTGATGAGAATATGTGCCCTGCCC

upper sequence: LOC_Os08g08220.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G43430.1 (Glycine max), 3'ss of exon 9
tgcaaatatccttgcccttcttgtttctatatctttggacaatcta-attactggt--gtaattcaatcttcttttgcaatctttggacttcttttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC
   | || |   |  |    ||    |  |||   |||    |  | | |||   |  ||  || |   ||  | ||     | ||   |    || |  ||||||   ||||| ||  | ||  | ||||||||||||||||||||||| ||||||||| |||  ||     | |||  |||||| || ||||| || ||  
---agattttgatttctcagttaacccgttatagatgggttgtaaacagtaccaatacgttgttaataattgctctggctgatatgttttgtggtttcaacagGATCCTCCTGAAGAGCCTGTTATTACGATGTGTGGCCATGTCTTCTGTTATCAATGTGTATCAGAATATTTGACTGGTGATGATAACATGTGCCCTTCAG

upper sequence: LOC_Os08g08220.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G23390.1 (Glycine max), 3'ss of exon 7
tgcaaatatccttgcccttcttgtttctatatctttggacaatcta-attactggtgtaattcaatcttcttttgcaatctttggacttctt--ttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC
   | || |   |  |  | ||    |  |||   |||    |  | | |||   |    |   |     |  |    |   |    ||  |  || |  ||||||   ||||| ||  | ||  | ||||||||||| ||||||||||| ||||||||| |||  ||     | |||  |||||| |||| ||| || ||  
---agattttgatttctctgttaacccgttatagatgggttgtaaacagtaccaatacgttgttaataattgctctggttgatatgttttgtggtttcaacagGATCCTCCTGAAGAGCCTGTTATTACGATGTGTGGTCATGTCTTCTGTTATCAATGTGTATCAGAATATTTGACTGGTGATGATAATACGTGCCCGTCAG

upper sequence: LOC_Os08g08220.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0071g00780.t01 (Vitis vinifera), 3'ss of exon 7
-tgcaaatatccttgcccttcttgtttctatatctttggacaatctaattactggtgtaattcaatcttcttttgcaatctttggacttcttttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC
 |    ||   ||| |   |  |  |  || |   |   |  |||| | |      |   |     || ||    || ||| |    |  |  |    ||||||  |||||||||||| || || || |||||||||||||| ||||||||||| ||| |||  ||     | |||  |||||| ||||  || ||| | |
gttttcattctcttactaatggttctattaaaaaatatcaatatctgaatggaaagggggtctgtcctactaactca-tctattatttgatgctcttacagGATCCACCTGAGGATGCTGTTGTTACCATGTGTGGCCATGTTTTCTGCTATCAGTGTGTATCAGAATATTTGACTGGTGATGACAATACATGCCCCGCAC

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|88311148|gb|CI658061.1|CI658061
EST:     TAAATTTGCTTGCAAAGCTGGAAGTTGGAGAGTTTTGTTCTGTATGCAGT                         GATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTAT
genomic: TAAATTTGCTTGCAAAGCTGGAAGTTGGAGAGTTTTGTTCTGTATGCAGTgtaagcaatc ... tttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattactggtgtaattcaatcttcttttgcaatctttggacttcttttacggcagGATGTACCTGAGGATGCCGTCGTGACGATGTGTGGCCATGTCTTCTGCTATCAATGTATATACGAGCGGATAACTACTGATGAGAATATGTGTCCCTCCC
 atctaat  putative branch site (score: 3)
                                        cttcttttac  putative PPT
           taattcaat  TA-rich tract