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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataattactggcacttaagttttcttcatcagcacaaattattgttcatgcatgcaacacaagaaaactcacctgacattctgatcgtgctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGAACGCCAAAGAACCCTCCTGTTTAATCCATAGTAAGCAACAAAGAGCAAA

Basic information

species Oryza sativa
transcript LOC_Os12g35350.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35350.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
aataattactggcacttaagttttcttcatcagcacaaattattgttcatgcatgcaacacaagaaaactcacctgacattctga--tcgtgctttgat---cagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAG---ATGGAAGGAAGAGCGGGAACGCCAAAGAACCCTCCTGTTTAATCCATAGTAAGCAACAAAGAGCAAA--
     |   || ||  | | |   | | | ||    |  || |  |||||||    |   |||    |  |   | |||  |     || | | |  ||   ||||||||||| ||||||||||||||| ||||||||   |||||     |||||  ||| || | ||| |||    ||  |    ||||| | | |||  | ||    
--cggtctgtgacatattaat---cctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCT----TTCCACGTGTAGTA-GTATCAAGAAACATTTT
















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|86488227|gb|CI130860.1|CI130860
EST:     CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG                         GTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
EST: gi|58612024|gb|CK039736.1|CK039736
EST:     CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG                         GTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
EST: gi|88256246|gb|CI358634.1|CI358634
EST:     CGACCCCCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG                         GTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
EST: gi|86824929|gb|CI358138.1|CI358138
EST:     CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG                         GTTTAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
EST: gi|86257277|gb|CI004095.1|CI004095
EST:     CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG                         GTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: CGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
EST: gi|86883096|gb|CI314294.1|CI314294
EST:     GACCCGCCGAGTTTTAGCGGGAGAACACGTCGAGGGCATTCCAGCTCCAG                         GTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA
genomic: GACCCGCCGAGTTTTAGCGGGAGAACA-GTCGAGGGCATTCCAGCTCCAGgtatttaaat ... ctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgcatgcaacacaagaaaactcacctgacattctgatcgtgctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGAACGCCAAAGAACCCTCCTGTTTAATCCATAGTAAGCAACAAAGAGCAAA
                aagaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataattactggcacttaagttttcttcatcagcacaaattattgttcatgcatgcaacacaagaaaactcacctgacattctgatcgtgctttgatcagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAGATGGAAGGAAGAGCGGGAACGCCAAAGAACCCTCCTGTTTAATCCATAGTAAGCAACAAAGAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA