Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgttgattcgttcgtgctagttcttagatgtgttcaattatacatacttcggaaaacattttatttttactgatgatggccctctgctctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATCTCATCACTTCAAAAAGATACAGGTCATGGCAAAAGCCACTCGAAAGGAT

Basic information

species Oryza sativa
transcript LOC_Os01g03070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G093050_T04 (Zea mays), 3'ss of exon 2
-acttgttgattcgttcgtgctagttcttagatgtgttcaattatacatacttcggaaaacattttatttttactgatgatggccctctgctctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATCTCATCACTTCAAAAAGATACAGGTCATGGCAAAAGCCACTCGAAAGGAT
 | ||    |  | |   ||| | ||||||    | | |   |||   |   | |  | | |   | | | | |||||     ||      | || |||||| || || |||||||| || |||||| |||| || ||||| |||||||||||||| || || ||||| |||||||||||||| ||||| ||||||| |||
caattaaaaaa-catggttgcaaattcttaagaatctgctcgtattggtgtgttgtcataaaagatgtgtatgctgatcgcttcctctgcttttatttcagAATTAATCCATGTTGGTCAAAAGCAGTCAGCCCTGCAGGCTTTACATGATCTCATTACCTCGAAAAGGTACAGGTCATGGCAGAAGCCTCTCGAAAAGAT
















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|88370850|gb|CI592616.1|CI592616
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88726955|gb|CI750610.1|CI750610
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88310182|gb|CI657606.1|CI657606
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTGGGGCAGAAGCAGGCAGCGCTACAGGCGTAACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88364312|gb|CI612261.1|CI612261
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88347801|gb|CI655154.1|CI655154
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88352152|gb|CI613803.1|CI613803
EST:     GGCCATGGCGACCTTCGCGAAAACTGAGAAAGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88730926|gb|CI754539.1|CI754539
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCACTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88314718|gb|CI608177.1|CI608177
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88390540|gb|CI609165.1|CI609165
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88316752|gb|CI624194.1|CI624194
EST:     GGGCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88736241|gb|CI759749.1|CI759749
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88719635|gb|CI743145.1|CI743145
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88423421|gb|CI576546.1|CI576546
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88312839|gb|CI589935.1|CI589935
EST:     GGCCATGGCGACCTTAGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|29626201|gb|CB631212.1|CB631212
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88421421|gb|CI569861.1|CI569861
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88403718|gb|CI611373.1|CI611373
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88731382|gb|CI754995.1|CI754995
EST:     GGCCATGGCGACCTTCGCGAAAACTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88352132|gb|CI613783.1|CI613783
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88316017|gb|CI618893.1|CI618893
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88311895|gb|CI577501.1|CI577501
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88389001|gb|CI595235.1|CI595235
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
EST: gi|88367768|gb|CI570507.1|CI570507
EST:     GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG                         AGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC
genomic: GGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGGgtgagtcccc ... tctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacttcggaaaacattttatttttactgatgatggccctctgctctacttcagAGTTGATACATGTTGGGCAGAAGCAGGCAGCGCTACAGGCGTTACATGATCTCATCACTTCAAAAAGATACAGGTCATGGCAAAAGCCACTCGAAAGGAT
                         tactgat  putative branch site (score: 2)
                                     ccctctgctctacttc  putative PPT
          aaaacattttattttt  TA-rich tract