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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacagaatgagttctttggaactagatttccatgttcaaaacttgtagctgttaaatcatgttaatccatacgtcttcttttccttctttggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAATGGGCCGATTACAATATTGATGCATATTTGGCTTCAACTCTGAAAACAA

Basic information

species Oryza sativa
transcript LOC_Os03g01890.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G109987_T05 (Zea mays), 3'ss of exon 11
cacagaatgagttctttgga-actagatttccatgttcaaaacttgtagctgttaaatcatgttaatccatacgtcttc-----ttttccttctttggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAATGGGCCGATTACAATATTGATGCATATTTGGCTTCAACTCTGAAAACAA
     |||  | |  |   | ||  |||||  |  |    |  || |     |  | ||    ||  | || | | ||      | || |||  ||||||||  |||| || || || ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||| |  |||| || |
---taaatatgctactgatatacacgattttaacat---gattttctgaacctagattccctatatgctatgcttttttaaacatgtttctttattggtattctagAGCGTCCCACCGGCAGTACTGGTACGATTTCTGAGGGAGCATAGATCTGAATGGGCTGATTACAATATTGATGCGTATTTGGCTTCATCATTGAAGACCA

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 12
--cacaga-atgagttctttggaactagatttccatgttcaaaacttgtagctgttaaatcatgttaatccatacgtcttcttttccttctttggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAATGGGCCGATTACAATATTGATGCATATTTGGCTTCAACTCTGAAAACAA
   || || || | | ||||  |||   |||||       |   |||    |  ||     ||| ||  || |        | || |||  ||||||||  |||| || || || ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||| | ||||| || |
gctactgatataaatgctttt-aacattatttctgaaccta--cctttcgtcctttcccatatggtatgcctttttaaacatgtttctttattggtattctagAGCGTCCCACCGGCAGTACTGGTCCGATTTCTGAGGGAGCATAGATCTGAATGGGCTGATTACAATATTGATGCGTATTTGGCTTCATCACTGAAGACCA
















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|58656979|gb|CK045659.1|CK045659
EST:     TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAG                         AGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA
genomic: TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAGgtaagggtaa ... ggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA
EST: gi|58685429|gb|CK074116.1|CK074116
EST:     TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAG                         AGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA
genomic: TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAGgtaagggtaa ... ggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA
EST: gi|58658713|gb|CK047393.1|CK047393
EST:     TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAG                         AGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA
genomic: TTGGAGCCCCCGGAGGTATTATATGTGCTAAGGCATCAATGTTACTGCAGgtaagggtaa ... ggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctgttaaatcatgttaatccatacgtcttcttttccttctttggtatttcagAGTGTTCCTCCAGCAGTACTGGTTCGATTTCTGAGGGAGCATAGATCTGAATGGGCCGATTACAATATTGATGCATATTTGGCTTCAACTCTGAAAACAA
              tgttaat  putative branch site (score: 3)
                          cgtcttcttttccttc  putative PPT
      ttaaatcatgttaat  TA-rich tract