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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgatggatgtgtgtgtgttttttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g47600.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G046587_T03 (Zea mays), 3'ss of exon 2
gtaactgatggatgtgtgtgtgttttttaaaagaaaatat-acaaacctt-ctctaacattgcttctttttctctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG
|||  | |   |||| ||     |||    |      ||| |  | | ||  ||||||||||  | |  |  | | |||  ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||
gtatttta---atgtatgcagcgtttcggtagccttttattatcagctttattctaacattg--tgtgctctttttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 5
-----------------------gtaactgatg--gatgtgtgtgtgttttttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG
                       ||  ||||||  ||   |    ||||| ||   ||  || ||   |||  | |  ||   ||    ||| |   ||     ||||||  ||  | ||||| |  ||||| || |||||||||||||| || |||||||||||||| |||
gtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttat---tctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 5
------gtaactgatggatgtgtgtgtgttttttaaaagaaaatata----------caaaccttctctaacattgcttctt---tttctctcctgata-gGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG
       |   | |      ||| | || |  |||| ||||||| |           ||||  |||      |||     ||    || | | |||| | |||||  ||  | ||||| |  ||||| || |||||||||||||| || |||||||||||||| |||
gtaccaatgcttaaaattgttgtttctgatacttaagagaaaatgtttgtttccagccaaaatttcaactgtattaaaatttgaacttttgttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG

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|163918159|gb|EG715273.1|EG715273
EST:     GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|163925750|gb|EG714586.1|EG714586
EST:     TGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: TGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|163926919|gb|EG715144.1|EG715144
EST:     GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58601442|gb|CK011970.1|CK011970
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|8404630|gb|AU091984.1|AU091984
EST:     GCACACTTTGTGAGGNCGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|15852955|gb|BI805751.1|BI805751
EST:     CACTTTGTGAGGACGGTTGACCCCCAGTGGACGTCCTCGTCCTGATGCAGG                         GAACAAGTTGTCCCGT-GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCA
genomic: CACTTTGTGAGGACGG-TGA-CCCCA-TGGACGTCCTCGTCCTGATGCA-Ggtaactgatg ... ctcctgatagGAACAAGTTGTCCC-TGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCA
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTNGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCAT
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCT-GGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCAT
EST: gi|88338355|gb|CI655544.1|CI655544
EST:     GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCT
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCT
EST: gi|163928605|gb|EG710890.1|EG710890
EST:     GAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58688425|gb|CK077112.1|CK077112
EST:     GCACACTCTGTGAGGACGGTGACCCCATGGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|58596788|gb|CK007316.1|CK007316
EST:     GGACGTCCTTGTCCTGATGCAG                         GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GGACGTCCTCGTCCTGATGCAGgtaactgatg ... ctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaagaaaatatacaaaccttctctaacattgcttctttttctctcctgatagGAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG
                       ctctaac  putative branch site (score: 2)
                   ccttctctaacattgc  CT-rich tract
     agaaaatatacaaa  TA-rich tract