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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgatcctagtggatttcatctgttagggtatactcatatgttctctcttataaatttcaacattggagtcttaactttatctttgtacctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCAATGTCCAACCCAACTACTAAAG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 12
---atcatgatcctagtggatttcatctgttagggtatactca--tatgttctctcttataa-atttcaacattggagtcttaactttatctttgtacctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCAATGTCCAACCCAACTACTAAAG
    || |  || |  |  ||   | |   | |   || |  |   ||  ||    || | |  | |  ||| | ||||  ||||   ||      ||  || ||||||||||| |||||||||||||||||||||||||| |||||| ||||||||||||||||||| ||||||||||
ccattcgttgtctttataaataagaccatattgtaaatcccaaatcatactccaagttgtcatgtgtttacaattgagtggtaaccccat------acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCAATGTCCAACCCTACTACTAAAG
















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|58596497|gb|CK007025.1|CK007025
EST:     CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
EST: gi|58601869|gb|CK012397.1|CK012397
EST:     CTCATGTGCTTGTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGGTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
EST: gi|29615205|gb|CB620218.1|CB620218
EST:     CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
EST: gi|29671881|gb|CB668156.1|CB668156
EST:     GTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: GTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
EST: gi|29662805|gb|CB659080.1|CB659080
EST:     CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
EST: gi|25799623|gb|CA755584.1|CA755584
EST:     CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA
genomic: CTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagaatca ... acctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcttataaatttcaacattggagtcttaactttatctttgtacctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCAATGTCCAACCCAACTACTAAAG
                           tcttaac  putative branch site (score: 2)
                                            tacctct  putative PPT
      ttataaatttcaacat  TA-rich tract