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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttggttttgtgatagcatgacaaaaactagagaggacaagtttgttgtgtttgcacacaaataatgagtttgttttctcattcatttgttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTGCCCCACCCCCTATTGCAAGTGTTGGGACTTTGGCTAAACAGAAGGCACC

Basic information

species Oryza sativa
transcript LOC_Os01g51200.1
intron # 12
splice site 3'
intron type U2

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|33679218|gb|CF307457.1|CF307457
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|58603326|gb|CK013854.1|CK013854
EST:     GGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: GGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|66913357|gb|CX100205.1|CX100205
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|218488633|gb|FG946946.1|FG946946
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGCTCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|33797259|gb|CF324492.1|CF324492
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|33678591|gb|CF306830.1|CF306830
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|33679446|gb|CF307685.1|CF307685
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAA-GACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|58682068|gb|CK070755.1|CK070755
EST:     AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: AGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
EST: gi|58672736|gb|CK061422.1|CK061422
EST:     ATTGCAAAACGACAGGCAGTCAG                         GTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG
genomic: ATTGCAAAACGACAGGCAGTCAGgtaattatct ... gttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtgtttgcacacaaataatgagtttgttttctcattcatttgttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTGCCCCACCCCCTATTGCAAGTGTTGGGACTTTGGCTAAACAGAAGGCACC
                                              ttatttt  CT-rich tract
                                     attcatttgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttggttttgtgatagcatgacaaaaactagagaggacaagtttgttgtgtttgcacacaaataatgagtttgttttctcattcatttgttattttagGTGTTGATGAAGGAAGGACTAGTGGTTGGTCATCAATGGATCGGCGCCGTGCCCCACCCCCTATTGCAAGTGTTGGGACTTTGGCTAAACAGAAGGCACC

- - - - -ttgtgat
- - - - - - - - -gcatgac
- - - - - - - - - - - - aaaaacta
- - - - - - - - - - - - - - - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaata