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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 3
gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
          | |    | ||  ||| |  | | | | |   ||  | |   |    |   | | | | |  |   |  || |  | || |||  | | | ||  |  ||    |||   ||| || ||||||||| ||||||||||||||| |||||||| |||||||||||||||||||  || |   || || |||| || | |||| |||| | | ||||||||||||
----------gtaaagcttgca-tatat-cgaaagggctaaatttatgcttcc---caggctctcacaaaattatacaatttt--caatttgaactaaccctt--gccctcttttttcaatttgtgctgcagCCAAATGAAAGCCTGTATGAGCAGAAACCAGAAGAGCCAAAACCTGCTGTACCTGCCTTGGCTGCTTCAACTAAAAAAGGTGGTCAGGCCTTGCATTCAC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 3
gtaacactgtggatcattagcgctatgtatgcatgtgtttggttccttcccacagttaatatttaatatacctcctctcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
                                  ||| | | || |   ||| |     || ||  |    | | |   ||  || |   ||   | | |  |   | || |  |||    || |  ||||||||| ||||||||||||||| |||||||| ||||||||||||||||||   || |   ||||| || | ||  ||||| |||| || |||||||||||||
----------------------------------gtgat-gcttgcagaccaaatgagctaatttgtgcttcccatgattttcattt---tggactaacccct---gccttatatttcaaattgtactgcagCCAAATGAAAGCCTGTATGAGCAGAAACCAGAAGAGCCAAAACCTGCTATACCTGCCTTGACTGCTCCAACTGCAAAAGGTGGTCCATCCTTGCATTCAC
















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|29677839|gb|CB674114.1|CB674114
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCC
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCC
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAAGC-AAAACCTGCTGC
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGA-GCCAAAACCTGCTGC
EST: gi|58670961|gb|CK059647.1|CK059647
EST:     AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAG                         CCAAAGTGAAAGCCTGTATGATCAGAAACCTGAA
genomic: AGATTGGAGGCAAGACTGGAGGGCTTGGTGTTAAAAAGCTCACCACAAAGgtaacactgt ... tatgttgcagCCAA-GTGAAAGCCTGTATGATCAGAAACCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctatctatatgatgtgaacattaaggactgacctttgcctttatgttgcagCCAAGTGAAAGCCTGTATGATCAGAAACCTGAAGAGCCAAAACCTGCTGCCCCAGTAATGACTACTTCCACCACAAAAAGTGGCCCGTCCTTGCATTCAC
                             gactgac  putative branch site (score: 2)
                                   cctttgccttt  CT-rich tract
     tatctatat  TA-rich tract