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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgcctgttgttgatgatgcaatgctaattattcaggttgcgattgagctttctgttgaggctgacattttcacacttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G149751_T03 (Zea mays), 3'ss of exon 11
gtccgtgcctgttgttg--atgatgcaatgctaattattcaggttgcgattgagctttc----tgttgaggctgacattttcacacttgct---cagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG---------------------------
||| || || | | | | || | |||| | || | | | ||| ||||| || | | |||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| |||
gtcagtaactagagcaagaacggtttgatttctggtgctcagagcaccgttttcttcttccgtttttggtactgacgttgctcctcccatcttccagGTTTGAGACTTGCTACCAGATCGCTCTTGCGATCAAGAAGGAAGTCGAGGATCTTGAGGCTGGTGGTATTCAGGTTATCCAAATCGACGAGGCTGCACTG
















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|300216253|gb|HO088038.1|HO088038
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGT
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGT
EST: gi|218478602|gb|FG965538.1|FG965538
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|218486860|gb|FG950334.1|FG950334
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|428194|gb|D24342.1|D24342
EST:     CCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: CCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|41884047|gb|BX928878.1|BX928878
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGGAGGTCGAGG
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGG-AGGTCGAGG
EST: gi|396941330|gb|HO188539.1|HO188539
EST:     TGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATC-AGAAAGGAGGTCGAGG
genomic: TGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAG-AAGGAGGTCGAGG
EST: gi|218501245|gb|FG948195.1|FG948195
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGA
EST: gi|58661898|gb|CK050578.1|CK050578
EST:     GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAG                         GTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAG
genomic: GGTCCCGTCACAATCCTTAACTGGTCTTTTGTCAGGAATGACCAGCCGAGgtccgtgcct ... acttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcaggttgcgattgagctttctgttgaggctgacattttcacacttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG
                              ggctgac  putative branch site (score: 3)
 cttgctc  putative PPT
 acatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgcctgttgttgatgatgcaatgctaattattcaggttgcgattgagctttctgttgaggctgacattttcacacttgctcagGTTTGAGACATGCTACCAGATTGCTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG