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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactagctgcatgatgcttgtttcttgcttctgtgttctatccagcctaactacctaatggtggaattgttaagaataattaactgacattcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGAATTGCATGACCTGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTA

Basic information

species Oryza sativa
transcript LOC_Os02g49980.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G089454_T03 (Zea mays), 3'ss of exon 3
tactagctgcatgatgcttgtttcttgcttctgtgtt--ctatccagcctaactacctaatggtggaattgttaagaataattaactgacattcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGAATTGCATGACCTGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTA
   |   || ||||   ||||| |     | | | |    |||  ||| | |||   || |  | ||   || | || |   ||| |      ||||||||||||||| ||||| ||||||||||| |||||||| || ||||| ||||||||||||| ||| |||||||||||||| ||||||||||||||||| || || 
-tgtgcgtgtatgactgttgttacccagatatttttcagttatatagctttactggata-tccttgatgggtcatgatttgataattttgtgacaattgcagATATGTTGTGGACGCTGCTGACCGAGATAGCATCCCAATAGCGAAAAGTGAATTGCTTGATCTGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTT

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G171060_T02 (Zea mays), 3'ss of exon 5
tactagctgcatgatgcttgtttcttgcttctgtgtt--ctatccagcctaactacctaatggtggaattgttaagaataattaactg-acattcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGAATTGCATGACCTGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTA
   |   || ||||   ||||| |     | | | |    |||||||||| |||  ||| |  | ||    | | |  |  |||| |      | |||||||| ||||| ||||| ||||||||||| |||||  | || || || |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || || 
--gtgtttgtatgaccgttgttaccgagatatttttcagttatccagccttactggcta-tccttgatggatcatggtttgttaattttgtgattaattgcagGTATGTTGTGGACGCTGCTGACCGAGATAGTGTCCCAATCGCGAAAAGTGAGTTGCATGATCTGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTT
















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|86512088|gb|CI154721.1|CI154721
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|8324374|gb|AU091530.1|AU091530
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|33817712|gb|CF334689.1|CF334689
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88342916|gb|CI640249.1|CI640249
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGAT
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGAT
EST: gi|88575977|gb|CI670122.1|CI670122
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATACCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|33808162|gb|CF329970.1|CF329970
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88345402|gb|CI656060.1|CI656060
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCA
EST: gi|33817714|gb|CF334690.1|CF334690
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|86600191|gb|CI251561.1|CI251561
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|55442549|gb|CV734564.1|CV734564
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|66923097|gb|CX109945.1|CX109945
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAA
EST: gi|86601190|gb|CI251570.1|CI251570
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|58665641|gb|CK054327.1|CK054327
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|88347247|gb|CI632532.1|CI632532
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACC
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACC
EST: gi|33818441|gb|CF335055.1|CF335055
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|58586064|gb|CF984372.1|CF984372
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
EST: gi|55414064|gb|CV726440.1|CV726440
EST:     AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCT                         ATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA
genomic: AGATTCCGGACCATGTGGGAGCGCTATTGCCGTGGAGTTTCTGCAATCCTgtaatttcct ... tcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaactacctaatggtggaattgttaagaataattaactgacattcaattgcagATATGTGGTGGATGCTGCTGACCGGGATAGCATTCCGATAGCTAAAAGTGAATTGCATGACCTGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTA
                                    aactgac  putative branch site (score: 2)
                   aattgttaagaataat  TA-rich tract