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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagtttctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA

Basic information

species Oryza sativa
transcript LOC_Os11g02830.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g02830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 5
gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagtttctgtt-ttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA
                                               ||  ||||||   ||      || |||||       | ||||      ||||| ||| |    |||||   |||| | |  |  ||  |    || || |||     | ||| | |  |||||||||||||||||| | ||||| || |||||||| || || ||||| || || ||| |||| ||||| ||||| ||||||||||| ||||||||||||||
-----------------------------------------------cttcatagcgaagtttatagccagcaaaaa------aaaaag------aagtgttattctta-atgcatgatctgatatcacatttata----cacctaatg-----acaccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA

upper sequence: LOC_Os11g02830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G007283_T01 (Zea mays), 3'ss of exon 5
gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagtttctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA
                                                     |||  | |  |   | | ||  |       | |||   || ||      ||||| | ||    | ||   | | || |  ||  | ||  | |||     ||||||| || ||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||||||||||||
-----------------------------------------------------agcaatgt--cttataaccagga-------aaaaaacgtattattcttaatgcatg-atctgatatcacatataccatcacacctacacttaatg-----atacctaatgtgcagGCCACTTGACTGCTAGAAGTGATGTCTACAGCTTCGGTGTGGTCCTTCTGGAGCTCTTGACAGGGCGCAAGTCAATCGACAAGTCGCGGCCCAGCAGGGA

upper sequence: LOC_Os11g02830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagttt--ctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA
                                                                    |||||    |   | | | ||| |      |   |||  | || |   ||   |  ||   |   |  |   | |  |||  | || ||||  ||     ||| |||||||| || ||||||||||| ||||||||||| ||||| ||||| ||  | ||||| ||  | || ||  | || ||| || | || ||||  ||
-------------------------------------------------------------------acatcatttcg-agctacatagtctctctttttgcatgacaataagtgcttagaccattacacaaataaacactaacttgac-tcta-atactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA

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|58680150|gb|CK068837.1|CK068837
EST:     ACGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATACGTGATGACTG                         GTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
genomic: TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTGgtactctcct ... tattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
EST: gi|25799597|gb|CA755558.1|CA755558
EST:     TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTG                         GTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
genomic: TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTGgtactctcct ... tattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
EST: gi|58685145|gb|CK073832.1|CK073832
EST:     TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTG                         GTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
genomic: TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTGgtactctcct ... tattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
EST: gi|313081121|gb|HO213707.1|HO213707
EST:     ACGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATACGTGATGACTG                         GTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG
genomic: TCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTGgtactctcct ... tattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttctgttttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA
                           atctgat  putative branch site (score: 4)
                                   tatatatacctatt  TA-rich tract