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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacctagctagcttagctagcttgacgaggtcggtgtgagatttggtagctcacgtttgatagctgattcgtgtgtttgtgtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGCAGCCATGCCTTCGTCGCCGACTTCCCGATGGCCGTTGATGACGACTTCG

Basic information

species Oryza sativa
transcript LOC_Os03g13520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152390_T05 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------------------gtatgtacctagctagcttagctagcttgacgaggtcggtgtgagatttggtagctcacgtttgatagctgattcgtgtgtttgtgtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGCAGCCATGCCTTCGTCGCCGACTTCCCGATGGCCGTTGATGACGACTTCG
                                                                                                              |||| |||| |  |||   ||||||      || | |||  |    ||||  || ||| |   |    |      || |     ||    |||||||| |||||| |||||||||| |||||||||||| ||||| | || |||||||| || ||||||||||||||||||   |||| ||| || |||  | 
gtaggccagccccaaacgcacgcacgcacgagcactcatcacgctctgttgtcgtcttagcttgtccctctctctctctctctctctctctctatctctctctctctccgatgt-cctatcccgctactctagctccgaccggcctgtgccatgcatggtt-ctgacgctgtgtgtgcgcacatcgtat---catggctatagGTTCTCTGGCCGCGGCTGGTGGCCAACAAGCTCTTCCGGAAGACCTCGGGCAGCCACGCTTTCGTCGCCGACTTCCCGGCCGCCGATGACGATGACGACA

upper sequence: LOC_Os03g13520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178279_T01 (Zea mays), 3'ss of exon 1
gtatgtacctagctagctt-agct--agcttgacgaggtcggtgtgagatttggtagctcacgtttgatagctgatt---------cgtgtgtttgtgtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGCAGCCATGCCTTCGTCGCCGACTTCCCGATGGCCGTTGATGACGACTTCG
       || |||||||   ||||    |  | |  |  |  | || ||  ||||       || |  ||    | |          |||||      || ||||||||||| |||||| |||||||||| |||||||||||| ||||| | || |||||||| |||||||||||||| ||||||    ||| ||  |||| |   |
-------ccgagctagccccagctccgacacggccggcgccctctgcgacatggttttgtgtgtattgtaatatactaacgctagctgtgtgcgcacatggggctagGTTCTCTGGCCGCGGCTGGTGGCCAACAAGCTCTTCCGGAAGACCTCGGGCAGCCACGCCTTCGTCGCCGATTTCCCGGCCACCGATGGCGACGGCGATG
















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|29640434|gb|CB645443.1|CB645443
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|88393484|gb|CI619776.1|CI619776
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29670691|gb|CB666966.1|CB666966
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29634762|gb|CB639771.1|CB639771
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29661801|gb|CB658076.1|CB658076
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29671559|gb|CB667834.1|CB667834
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29634757|gb|CB639766.1|CB639766
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29671784|gb|CB668059.1|CB668059
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|29668856|gb|CB665131.1|CB665131
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
EST: gi|58688536|gb|CK077223.1|CK077223
EST:     TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAG                         GTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC
genomic: TACCTCCCTACGGATTGGTCGCCATGCTAGAGAACCAGAGGCAAGCGGAGgtatgtacct ... gtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagatttggtagctcacgtttgatagctgattcgtgtgtttgtgtgtggctagGTTCTTTGGCCGAGGCTGGTGGCGAACAAGCTCTTCAGGAAGCCATCCGGCAGCCATGCCTTCGTCGCCGACTTCCCGATGGCCGTTGATGACGACTTCG
                    tttgata  TA-rich tract