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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttctcttgatcagtaacagtctcctacagtttcttactgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctcttgtttctttgattaattgctttatag

Basic information

species Oryza sativa
transcript LOC_Os05g37170.6
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37170.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G000842_T02 (Zea mays), 5'ss of exon 4
CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttct-cttgatcagtaacagtctcctacagtttctt-actgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctct-tgtttct-ttgattaattgctttatag
                 |||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||  || |||| |  ||||  ||||||||| |||  |||||   ||| | | ||| ||||||||| ||||||| |||||||||| || || || | || | || |||||  ||||||    ||
-----------------CAGCTGGATACCTTGCAGCTAGGCCCCCCACACTGGAGATCTTCCCTTCATGGCCAATGAGTCATCTACAGCAGCCATACAGTgtaagcactgtttctgtttcatcattcgcagtgccctacagttcctttgctgacca-aaccggacaaaggtgttcttggttaattaactgctcactgccttcttctgtctgctcctcttgatggattgctgcgcag

upper sequence: LOC_Os05g37170.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G09430.2 (Glycine max), 5'ss of exon 3
CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttctcttgatcagtaa-cagtctcctacagtttcttactgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctcttgtttctttgattaattgctttatag
                    |||  |   |  |||  |||||  |   |||||||||||| ||||| ||||||||||||||    |  ||     ||       ||  |  |   |||||   ||| |   |  |||   ||   | | ||   |  |   |  ||||  || |      ||| | ||    | || | | |                                  
--------------------CAGCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGAgtactactctgtctctctctctctcacttctccatctttgaccaatccatatccatagatgcttaaaactagcgc---aacttcaataatatcccaatctttt---------------------------------

upper sequence: LOC_Os05g37170.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G09430.3 (Glycine max), 5'ss of exon 4
CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttctcttgatcagtaa-cagtctcctacagtttcttactgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctcttgtttctttgattaattgctttatag
                         |   |  |||  |||||  |   |||||||||||| ||||| ||||||||||||||    |  ||     ||       ||  |  |   |||||   ||| |   |  |||   ||   | | ||   |  |   |  ||||  || |      ||| | ||    | || | | |                                  
-----------------------CTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGAgtactactctgtctctctctctctcacttctccatctttgaccaatccatatccatagatgcttaaaactagcgc---aacttcaataatatcccaatctttt---------------------------------

upper sequence: LOC_Os05g37170.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA12G30990.1 (Glycine max), 5'ss of exon 4
CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttctcttgatcagtaacagtctcctacagtttcttactgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctcttgtttctttgattaattgctttatag
                         |   |  |||| || ||  |    ||||||||||| ||||||||||||||||||||    |  ||    ||| | |||   ||         | |  |||  | ||  | |  |  |   |  |  | | |||          | |  | |  | | ||  |    |||| | | |  |  | ||                         
-----------------------CTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCA-AGAgtactagtctcctacttgtccatctttgaccatttatttaaacatgcttttaattgctt--------atgcttacaagttcaagaaat--ctcaatattttatttttttt------------------------

upper sequence: LOC_Os05g37170.6 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0080g00360.t01 (Vitis vinifera), 5'ss of exon 4
CATTTGTATGTATGCAGCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactgcttctcttgatcagtaacagtctcctacagtttcttactgactgcaacagaaaaaaagtgttcttgcttaattagctgctcactgtctgctcctcttgtttctttgattaattgctttatag
                         |   |  |||| |||||  |    || |||||||| ||||||||||||||||||||     | ||| |  |  | || |||        || |||  |||  | ||  | || |    ||  ||| | ||   || |    || |   |   || |   |       ||  | ||| || ||  || |                      
-----------------------CTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGAT---TCCAGCAAACCCAAAGAgtag-------ttttctccatctttgaccatttcttt---ttcattaataaccttaatactgcaacatcctctctggtctctacaactttccttctcttctactggtgct----------------------

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|88364529|gb|CI644607.1|CI644607
EST:     TGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT                         CAGAACTCGCAGTCAGTAGGGAGCACCACTGACTCTAGCTCAGCTCAGAAC
genomic: TGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactg ... tgctttatagCAGAACTCGCAGTCAGTAGGGAGCACCACTGACTCTAGCTCAGCTCAGAAC
EST: gi|33655991|gb|CF278605.1|CF278605
EST:     TGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT                         ---AACTCGCAGTCAGTAGGGAGCACCACTGACTCTAGCTCAGCTCAGAAC
genomic: TGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGTgtaagcactg ... tgctttatagCAGAACTCGCAGTCAGTAGGGAGCACCACTGACTCTAGCTCAGCTCAGAAC