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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagcgtacatagcatatgtgatgagctgtattgaaattcctatctgttctctggtgatatcctatctgtgttctgatgatgttgcattgttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAAAGGATTATGTGCATGTGCGCATCCAGCAGCGCAACGGCAGAAAGAGTCT

Basic information

species Oryza sativa
transcript LOC_Os05g41900.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41900.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G073535_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------------aacagcgt-acatagcatatgtgatga-gctgtat---tgaaattcctatctgttct--ctggtgatatcctatctgtgttctgatgatgttgcattgt-tttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAAAGGATTATGTGCATGTGCGCATCCAGCAGCGCAACGGCAGAAAGAGTCT
                                                                                   || ||  | ||  |  | || |||| |     ||     ||| ||| | |      |   |  |  | | || | ||  | |||||| | | ||||  | ||||||||||||||||||||||||||||||||||||||| || ||||| |||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||
gtatggctacttctcaattcatgatgccatgtttttttttatattgtggttttacataatacatagcatcttccagcttcctgaagagtattactgaatagat-tgataacatcatacacacgaagttcatcttgaacatgcttattagtgttctgtttgcat-ctgatggtatggcatcatctttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCTGGTGCTGGTCCTGGAACGAAGGATTATGTGCATGTGCGCATCCAGCAGCGCAACGGCAGAAAGAGTCT
















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|58588869|gb|CF987177.1|CF987177
EST:     AGAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|396941233|gb|HO188442.1|HO188442
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|88326135|gb|CI651190.1|CI651190
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|33666834|gb|CF297801.1|CF297801
EST:     ATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGGGCGCTGGCCCTGGAGC
genomic: ATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCC--GGCGCTGGCCCTGGAGC
EST: gi|88976349|gb|CI024566.1|CI024566
EST:     ACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58587133|gb|CF985441.1|CF985441
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29685126|gb|CB681401.1|CB681401
EST:     CGACGTTCAGCTTCCCTCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|86260752|gb|CI000200.1|CI000200
EST:     CTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29687847|gb|CB684122.1|CB684122
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58591899|gb|CF990207.1|CF990207
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|29687846|gb|CB684121.1|CB684121
EST:     ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|58607649|gb|CK035682.1|CK035682
EST:     ACAAGCGAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: ACAAACAAGTTTCATGTCTGATCTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|33692899|gb|CF321138.1|CF321138
EST:     GTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: GTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
EST: gi|89198573|gb|CI016658.1|CI016658
EST:     CTCGACGTTCAGCTTCCATCTGCCTTCG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA
genomic: CTCGACGTTCAGCTTCCATCTGCCTTCGgtacgcttca ... gttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttctctggtgatatcctatctgtgttctgatgatgttgcattgttttgatagATCCGTTTGCTGAGGCAAATGCTGAGGACTCCGGCGCTGGCCCTGGAGCAAAGGATTATGTGCATGTGCGCATCCAGCAGCGCAACGGCAGAAAGAGTCT
                           ttctgat  putative branch site (score: 3)
                                           ttgtttt  putative PPT
                                          attgtttt  TA-rich tract