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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgttaattgaaatctttaattttcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM5G873287_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------gtatcctgttaatt-------gaaatctttaattttcgtttggtacttgaaaca----------ttgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
                                                  | | |||  |||        |||||  |   ||| ||||  ||||  | ||           ||| | ||||||| ||    | |   |   | | ||| |||       |||  |||    ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||  | | 
gtatctccacatttccattccaccagttaactgatatgtgtgctattgacaccttgtggatttcatctcaaaatccctctattttgtttattactcaatactcatgattttcttgggaagtgggactggttcacttaattagagacgatctatc------tgctaaac---attactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 19
----------------------------------------------gtatcctgttaat-------tgaaatctttaattttcgtttggtacttgaaacattgtgg--agtgggattgaccta-ttgggtataaaatgatgtatgattgtatgcctaactgtt--ttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
                                                | | |||  ||         |||||  |   ||| ||||  |||||   |  || |||  ||||||| ||||| | ||   || | | | | || |||  | |   ||| ||| |  ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||  | | 
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttga--gaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G350256_T01 (Zea mays), 3'ss of exon 3
gtatcctgttaattgaaatctttaattttcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgccta-actgttttactttttccttcatcagGAGGCAAATAAGAGGAACA-ACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
                                                                              |   | |||||  | | | |||| |   | ||| | |     | ||     | || ||       ||| |  |       | |  |   |     |  |   ||||| |||||||||||||||||||||| |||||| | || | 
---------------------------------------------------------------------------cttagcaacgtatggatatttacctatataatattagtgtcatagtgatattttgtcacatggattctacatattatatatctctattttttt--attcccgTGACAATGTCTATCCTTGGATTCAACGAGTTTATGACACTATTGAT

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
                  | | ||  || | || |  |   | |    || |  | |  |  | ||     |   |  || ||| || | | | |      |      ||   |||        ||||| || ||     |||| ||||||||||||||||||||||||||| |    ||  ||| | | |||||||| || || || |||||  | |||| 
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG

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|87022912|gb|CI269848.1|CI269848
EST:     ATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
genomic: ATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|29641074|gb|CB646081.1|CB646081
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAN                         GAGGCAAATAAGAGGAAACA-CAACTGGCTGCCACCTCCAT
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAA-CAACAACTGGCTGCCACCTCCAT
EST: gi|88340407|gb|CI659613.1|CI659613
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|157650537|gb|EX450171.1|EX450171
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGTACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|38474188|gb|CF958320.1|CF958320
EST:     CATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCACATAAGAGGAACAACAACTGGCTGGCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|58690187|gb|CK078874.1|CK078874
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
EST: gi|218485492|gb|FG956827.1|FG956827
EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
                         gcctaac  putative branch site (score: 2)
                               ctgttttactttttcc  CT-rich tract
                                  ttttacttttt  TA-rich tract