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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacgctactattgcatggtccttttccacttcagttggcatattcagaaccattttggcaaaccacttggatttattctcttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g07720.4
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 12
gtaacacgctactattgcatggtccttttcc---acttcagttggcatattcaga-accattttggcaaac-cacttggatttattct----cttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT
                  ||  | ||||| |   |  | || || | | |  | | |     |||| ||     | |  ||||  |||     |||| |||   ||| |  || |  |||| | ||| ||||||| | |||||||  |||||||||| | || ||||||||||||||||| ||||| || ||||||||  | ||| | | ||| ||||||
------------------attcttctttttctgaaactaagatgccgtctctaaacagtgcgttggaaagtattcatttatttggtctgcaatttatttcatttcccctcatttt--cagGATTATTCTATTTCTCGTTGTGGAGTGCTGCTGGAATGTTTACCCTTCCACTGCCTATTCATCACTCCTTTTGCTATTTGTGCACTTGTGCATTTTGTTT

upper sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA03G37130.1 (Glycine max), 3'ss of exon 11
gtaacacgctactattgcatggtccttttccacttcagttggcatattcagaaccattttggcaaaccacttggatttattctcttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT
              | |  |   ||   ||| || |  || |  ||||       |   |   |      || ||||  |    | ||        |   |||||   |||  | ||||| ||  | |  |||||||| |||||||||||||||||||| |    |  ||| |||  | |  | || |   ||||||     ||  | |  
-------------gtagattaacccacatcccctgct-ttcgtttatttttgttaacgattttattttgttttgattcgtaaa-taatcgatttctctcatgttcaagcagTTTGATTTTGTTCGTGGGAGTGGAGCTGTGCTGGAATATCTATCCTTCGAACAGCCTTTCTTCAGCGTTACTTCTTTGTCTTCACACAATTATTCTCTGG

upper sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA19G39740.1 (Glycine max), 3'ss of exon 11
gtaacacgctactattgcatggtccttttccacttcagttggcatattcagaaccattttggcaaaccacttggatttattc-tcttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT
               |  |    | |      |||  |||    | || | ||| |||||          ||| |||| |   |    |||  |  |    || ||   |||  | ||||| ||  | |  |||||||| |||||||||||||||||||| |    |  ||| ||| ||||  | || | | ||||| |    ||  | || 
----------gtaggttaacccacatcccatgctttcgtttattt-tttaaaacgattttattttgtt--ttgaatttgtaaataacgtatttct-ctacatgctcaagcagTTTGATTTTGTTCGTGGGAGTGGAGCTGTGCTGGAATATCTATCCTTCGAACAGCCTTTCTTCAGTGCTACTTCTTTGCCTTCACTTAATTATTCTCTTG

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|89162652|gb|CI099344.1|CI099344
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|89193425|gb|CI050723.1|CI050723
EST:     CTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: CTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|88247507|gb|CI247356.1|CI247356
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|86499763|gb|CI142396.1|CI142396
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|33800779|gb|CF326261.1|CF326261
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|89161465|gb|CI099437.1|CI099437
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|88228317|gb|CI227797.1|CI227797
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|163925452|gb|EG711565.1|EG711565
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|88484104|gb|CI421375.1|CI421375
EST:     CGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: CGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|86492318|gb|CI134951.1|CI134951
EST:     TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TATTCACTGCCTTTCCTTTTGTGGAAAACTCGTTTTCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
EST: gi|86420213|gb|CI055014.1|CI055014
EST:     TCCAACATTTGTGAG                         GGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC
genomic: TCCAACATTTGTGAGgtaacacgct ... gttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggcaaaccacttggatttattctcttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT
                                    ccgccctttgttctct  CT-rich tract
                  atttattctcttatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacgctactattgcatggtccttttccacttcagttggcatattcagaaccattttggcaaaccacttggatttattctcttatatcaccgccctttgttctctcagGGTCATTTTATTTCTTGCTGTGGAGCTCTGCTGGAATATCTATCCTTCCACTGCCTATTCGTCACTGCTGTTGCTATTCATTCACATCTCCATCTTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT