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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatgtttatattcccttgggcttatattacatagacttgtgtatgaccaatgcaatgctaatgtttatgatcctcctctagcatgttctaactgaatttattggtttgcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAAATCCTTGGTCCTTCTCTGGTTGCCCTCTACAATCCACTCCAACCAGCAT

Basic information

species Oryza sativa
transcript LOC_Os06g49500.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49500.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G134930_T02 (Zea mays), 3'ss of exon 4
gtaagcatgtttatattcccttgggcttatattacatagacttgtgtatgaccaatgcaatgctaatgtttatgatcctcctc-tagcatgttctaactgaatttattggtttgcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAAATCCTTGGTCCTTCTCTGGTTGCCCTCTACAATCCACTCCAACCAGCAT
                                    ||   || ||  |     ||   |   ||   ||    |||  |||  | |  |   ||  ||   | ||      ||| | || ||||| | ||||| || ||| |||| ||||| |||||||| ||| | ||||| ||||| || || |||||||| ||||||||||| ||||||||||| ||||
-----------------------------------gtaagtttctgagt--ttgatattagattacatttcgaaatctccctggttgtgtaaccttgct---tctacctacctgcctgac-agGGAGTCGTTGCGTCCTGCCTGAACTACGCGATCATGACCTGGGCGAACAAGATCCTCGGGCCGTCTCTGGTCGCCCTCTACAACCCACTCCAACCGGCAT
















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|218487115|gb|FG960498.1|FG960498
EST:     TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCT                         GGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA
genomic: TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCTgtaagcatgt ... gcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA
EST: gi|58609279|gb|CK037312.1|CK037312
EST:     TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCT                         GGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA
genomic: TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCTgtaagcatgt ... gcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA
EST: gi|33682871|gb|CF311110.1|CF311110
EST:     TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCT                         GGAATTGTAGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA
genomic: TCCATGAATGGGCATTGACAACGACCGAGATCATTGCTATTCTATATGCTgtaagcatgt ... gcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatgatcctcctctagcatgttctaactgaatttattggtttgcttcaccagGGAATTGTTGCATCTTGCTTGAATTACGCAATCATGACTTGGTCAAACAAAATCCTTGGTCCTTCTCTGGTTGCCCTCTACAATCCACTCCAACCAGCAT
                       ttctaac  putative branch site (score: 1)
                                          tttgcttc  putative PPT
                          taactgaatttatt  TA-rich tract