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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacttactcatcatgcttgcatgttgcatgatcatatctagatacacaatcatcatcacatctgccaaaatattcatttgtaaattagcagctcgagttaatgcgtttttcttttctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCGTTTCGACATTCATCATTACATGCTCTGTATTTTGGTTCTGTTTATGTAT

Basic information

species Oryza sativa
transcript LOC_Os04g11820.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11820.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G455476_T01 (Zea mays), 3'ss of exon 9
gtattacttactcatcatgcttgcatgttgcatgatcatatctagatacacaatcatcatcacatctgccaaaatattcatttgtaaattagc--agctcgagttaatgcgt-ttttcttttctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCGTTTCGACATTCATCATTACATGCTCTGTATTTTGGTTCTGTTTATGTAT
                 |   | | |||| ||| |   | |||   |  |     |   |     ||      || | | | |   |||  ||  | || |   |||||    |||| |  | |  | ||||||||||||||||||||||||||| ||||||||  |||||||    ||||  || || |||||  | |||| |||||| |||||| || |||| ||||||
----------------gtaagtacttgtt-catcactgtctct---tttatggctacagtttttgctttatgcatgtccctgttgtaatgcgctgaacttgtactaatggaaattttatcattttgtccagGTATCCTGGAGTTTGGCTTATAACCCGCTGTGGCCTGTTGTTTCAGAGTCAATTTGATATTCACAACTACAAGCTCTGCATTTTGATTTTGTTCATGTAT
















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|88383068|gb|CI538096.1|CI538096
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88453441|gb|CI563320.1|CI563320
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88255823|gb|CI353694.1|CI353694
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88234008|gb|CI233857.1|CI233857
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88233917|gb|CI233766.1|CI233766
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|89194779|gb|CI003243.1|CI003243
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCCAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88235761|gb|CI234963.1|CI234963
EST:     TGCTATCCCAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|29672932|gb|CB669207.1|CB669207
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|86842427|gb|CI335307.1|CI335307
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|88233937|gb|CI233786.1|CI233786
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
EST: gi|86480263|gb|CI122896.1|CI122896
EST:     TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAG                         GTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG
genomic: TGCTATCCAAAGTGGGCATTAGAGGGTTTCATAATTGTAAATGCAAAAAGgtattactta ... tctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcatttgtaaattagcagctcgagttaatgcgtttttcttttctatttcagGTATCCTGGAGTTTGGCTTATAACTCGCTGTGGGTTGTTGTTCAGAAGTCGTTTCGACATTCATCATTACATGCTCTGTATTTTGGTTCTGTTTATGTAT
                          agttaat  putative branch site (score: 4)
                                tgcgtttttcttttct  CT-rich tract
                                    tttttcttttctattt  TA-rich tract