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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT

Basic information

species Oryza sativa
transcript LOC_Os12g03720.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G180155_T01 (Zea mays), 3'ss of exon 3
----------------------gtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaagg----agttcctctaaaca---tcttcacctcttgca-----gCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGG---CGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT
                      |  |      ||| |||  |   |     | | | |  | |   |    | ||||    || |        |    |   |||||||||||     ||||||| ||||| ||||| ||||||||||| || |||||||||   |  | ||||||||||||||| | ||| |||||  | ||    |||  || ||   | 
gtaacgctgaaaccgtgttctcgggaagaacctggtcagtttt--ggttgtgcttagtaacatgaaacccctgaaggctgaagctagctggggctggtttcccacctcttgcattgcagCAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGCAAGGGGACGCCGCCGATAGTGATGTGCTCGAGGGGGGACGCCACCGCG--CTGCTGTA-TGCCCCA

upper sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G005849_T01 (Zea mays), 3'ss of exon 9
gtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT
||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   ||||||||||||||||| ||||| ||||| || |||||||| || |||| |||||| ||||||||||||||||| | |||||| ||  | || || |||||||| ||    
gtaatga---taaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG
















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|86426649|gb|CI071746.1|CI071746
EST:     GATGAAAACCTTCCGATGATCGTCATTGCTACACGTGATGCGTGCCTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88902738|gb|CI088276.1|CI088276
EST:     TACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: TACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58600045|gb|CK010573.1|CK010573
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86479812|gb|CI122445.1|CI122445
EST:     GATGAAAACCTTCGGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|89184705|gb|CI007130.1|CI007130
EST:     GATG-AAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|87026077|gb|CI250093.1|CI250093
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86834864|gb|CI345948.1|CI345948
EST:     ACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: ACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88837681|gb|CI079041.1|CI079041
EST:     GCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|3766919|gb|AU031029.1|AU031029
EST:     GATGAAAA-CTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86496093|gb|CI138726.1|CI138726
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86481498|gb|CI124131.1|CI124131
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88902955|gb|CI088493.1|CI088493
EST:     CTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: CTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT
                              ctctaaa  putative branch site (score: 3)
                                     catcttcacctctt  CT-rich tract
     tttcttttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA