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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatttttctcccattcaacaatttgtacatttcagttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag

Basic information

species Oryza sativa
transcript LOC_Os11g08330.1
intron # 29
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G115245_T01 (Zea mays), 5'ss of exon 13
TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatttttctcccattcaacaatttgtacatttcagttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag
||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| || || || ||||||||||||||||||||||||||   ||| | | || || |  |  ||  |||| |  |||  |   ||  | ||| ||    |  |  | ||  |  |   |     |              
TTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAGgtttgctgctttcccctcaatccaacacctgctcattac--ttg-gttccagtcacaagattaa-aactcgtatgcaatcgaaccactgcag--------------

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA06G16110.2 (Glycine max), 5'ss of exon 29
TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatttttctcccattcaacaatttgtacatttcag--ttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag
| ||||||||||||||||| ||||||||| | ||||| ||||| |||||||||||||| || ||||||||||| ||||||||||| ||||     || ||  | |  || || | | | | ||||   |  |||| ||   |     || |    |||        || | |   |   |  | || | ||   | 
TGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACCAGgt-----atgttcattcagttaaatattatat-cattgagggattgcttggggggctagagttctcagatttttggttttaagaggcacaatatttcagt-attaaa-

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA04G38800.2 (Glycine max), 5'ss of exon 13
TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatttttctcccattcaacaatttgtacatttcagttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag
| ||||||||||||||||| ||||||||| | ||||| ||||| |||||||||||||| || ||||||||||| |||||||||||||||| ||    |||  |   ||   | | |   |     |   |||| ||   |     || |    |||        || | |   |      | || |  |     
TGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACAAGgtatgttcatttagtgaaatattata-tcattgaggattgattgcttggggggctagagttctcagatttttggttttaagaggcacaactttacagtatt-----

upper sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 29
lower sequence: AT5G63960.2 (Arabidopsis thaliana), 5'ss of exon 29
TTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgcc---atttttctcccattcaacaatttgtacatttcagttgcatgttagctataagcttcttgatccacaagctttaaatttatgttggtgcaatgatcgcag
|  ||||||| ||   | | ||||||||||| ||||| |||||||||||||| |||||||| |||||||| || ||  | ||||| ||||||||    |||||| ||    ||||    || || |  ||  |     | ||  ||    ||  |  |    |     |  | ||  | ||||| |  | |  |   
TGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAGgtttgcttatatttttatcgatatcaatttcttttagaaatctttcagcaggtaaataggttctgatccaatttcctttctggatttcttattggt-cttttacag---

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|58654042|gb|CK042722.1|CK042722
EST:     CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG                         CCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
genomic: CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatt ... atgatcgcagCCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
EST: gi|88959740|gb|CI002350.1|CI002350
EST:     CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG                         CCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
genomic: CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatt ... atgatcgcagCCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
EST: gi|88841192|gb|CI080646.1|CI080646
EST:     CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG                         CCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
genomic: CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatt ... atgatcgcagCCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
EST: gi|9865734|gb|AU101484.1|AU101484
EST:     CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG                         CCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC
genomic: CAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAGgtttgccatt ... atgatcgcagCCGGGATTGTCCTATTTTCTACCGCCGAAGAAAGGCGCAGAAGGATATGGC