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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttattcaggtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT

Basic information

species Oryza sativa
transcript LOC_Os03g38590.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38590.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 12
gtgggttattcaggtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT-
                       || ||  | |  |   | |  |||||      |  | |   |||  |   ||        || |   ||| | ||  | ||   ||  |  |    |||||||||||| || || |||||||| || || ||||| || || ||||||| ||| || || |||||||| || |||||||| || |||||| ||    ||  || 
-----------------------gtgtgaagttactaaatat--gttgctctc-ctattcatctcttgacaccttc-------aattggttctgaactgttaagttttgc-caacacctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGA-ACCGTGTGTG

upper sequence: LOC_Os03g38590.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G011078_T02 (Zea mays), 3'ss of exon 11
gtgggttattcaggtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGAT-GTACGT
                       ||    |  |   |   | | | | | |  || |||   | |||  |   ||         | ||  |       ||| |   || |||  ||||||     ||| || || || |||||||| || ||||||||||| || ||||||| ||| || || |||||| | ||||||||||| ||||||||||||  |  |||   
-----------------------gtgaagttattactgcctaccgcttcattgatctct--cttcttgacaccttc--------agttggttctgaactgtaaaagctctgcatcctgca-----gCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA-
















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|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|88832975|gb|CI369865.1|CI369865
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCAT                         G
genomic: TTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATgtgggttatt ... tgcactgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT
                  atctaac  putative branch site (score: 2)
                                      tgctccct  putative PPT
           aaaatttatctaa  TA-rich tract