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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA

Basic information

species Oryza sativa
transcript LOC_Os03g16980.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 8
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || |||                                 
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG---------------------------------

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 9
gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA
|||||||| | |||| |   || |   |  || ||| || || |||| | ||  ||| |  || | |  | ||| || ||  |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||| || || |||                                 
gtaatgcttgttgaattc--tttagtttcttcccagcttctg-ccagatagttttggtggctaatatt-ttcatgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG---------------------------------

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 5
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| ||||||                                                         
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGG---------------------------------------------------------

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 15
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA-
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| |      |  ||| || ||  | || ||| ||  || ||  ||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || || |||||||  ||     |   |   |||  ||   
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatatattggcggctaatctt--ttcacaatctt-tagCGGTCAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATAGTTTGTCTTCCACCGCGTTCT-CAATTGGTTTGT

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 10
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA
||||||||  | ||||  | ||| |   ||||||   | |   | ||| |      |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || ||||||||||  ||  |        |  | ||||  
gtaatgctttgttgaatgtatttta-ttttctcttgagctac-tgcagatatattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATGGTTTGTCTTCCACT-----GCATTCTCAATTG-

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|33680606|gb|CF308845.1|CF308845
EST:     ACATTGATGATGGGCNGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: ACATTGATGATGGGC-GTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|38478163|gb|CF962296.1|CF962296
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|33675428|gb|CF303667.1|CF303667
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29668646|gb|CB664921.1|CB664921
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|30226636|gb|CB964528.1|CB964528
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTACATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAAC-CAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29668686|gb|CB664961.1|CB664961
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA
                               ttattttcatacataa  TA-rich tract