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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGATTATGGGAGGTGCATAGCAGAAAAGGTCCCTGAGATTGAACAAAATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttttgtcattaagcaaacagggtgatcccataaaatcatgctattacatccatatacttaagtaaccaatttaattaaatgcaaagggccaaa...

Basic information

species Oryza sativa
transcript LOC_Os10g26140.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g26140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G444692_T02 (Zea mays), 5'ss of exon 1
AAAAGATTATGGGAGGTGCATAGCAGAAAAGGTCCCTGAGATTGAACAAAATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt-tgtcattaagcaaacagggtgatcccataaaatcatgctattacatccatatacttaagtaaccaatttaattaaatgcaaagggccaaa-----------
||||||||||||||| |||||||||| ||||||||||||||||||||| ||||||||| | ||||||||||||||||||||| |||||||||||||||||||||||| | | |||||| |||| | | | ||| | ||| | |||||||||| || ||||||| ||| || ||||||
AAAAGATTATGGGAGATGCATAGCAGCAAAGGTCCCTGAGATTGAACATAATATGTGTTCCAAGGAGTTTCTAGCACTCAGAGCATGCATGCAGACTGTGgtaatttcctgcgccattaaacaaatatataggc----ttgaattac----ttaggtgcatatacttatgtgtccaatttgt----atgtaaggggccattatcctcagcac
















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|88351657|gb|CI617382.1|CI617382
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
EST: gi|88426630|gb|CI579459.1|CI579459
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCG
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCG
EST: gi|88449558|gb|CI579838.1|CI579838
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGGAGACTGTG                         GTCAAGCGCAAGGCTTGAAGT
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGT
EST: gi|88407793|gb|CI607927.1|CI607927
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTC
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTC
EST: gi|117245650|gb|CT848471.1|CT848471
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
EST: gi|29634116|gb|CB639125.1|CB639125
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
EST: gi|88390435|gb|CI607471.1|CI607471
EST:     TATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCCTTTCGGAATTTGAT
genomic: TATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGC-AGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGC-TTTCGGAATTTGAT
EST: gi|29630281|gb|CB635290.1|CB635290
EST:     ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTG                         GTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT
genomic: ATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttt ... atcctgaaagGTCAAGCGCAAGGCTTGAAGTTCTGGAGTTAAAGCTTTCGGAATTTGATAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGATTATGGGAGGTGCATAGCAGAAAAGGTCCCTGAGATTGAACAAAATATGTGTGCTAAGGAGTTTCTAGCACTCAGATCATGCATGCAGACTGTGgtaatttttttgtcattaagcaaacagggtgatcccataaaatcatgctattacatccatatacttaagtaaccaatttaattaaatgcaaagggccaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA