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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGCCGCCGTCATCGCGCACGCCTTCCGCCGCGGCGTCACCTTCTTCGACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcggggcccttcccttccttcatcgttcgtggtttcttgtggttggattggatgatgatgagctaaccccatcgccttcggatttccag

Basic information

species Oryza sativa
transcript LOC_Os01g43090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 2
CGGCGCCGCCGTCATCGCGCACGCCTTCCGCCGCGGCGTCACCTTCTTCGACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcggggcccttcccttccttcatcgttcgtggtttcttgtggttggattggatgatgatgagctaaccccatcgccttcggatttccag
||||  |||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||| |||||| ||||||| |||||||||||||||||  | ||| |  | |||| |  |   | | |  |||       | ||||   |     |  || ||  |  |  | |  |  |  |  || |||
CGGCATCGCCGTCATCGCGCACGCTTTCAGCCGCGGAGTCACCTTGTTCGACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgcg--ctttccttaaccagagcctgtgtgagc----gaggtttactgacccgcggaagacattgctgcctgtctgtgtgcgttgcag
















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|88421693|gb|CI586662.1|CI586662
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|58689204|gb|CK077891.1|CK077891
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88447787|gb|CI576983.1|CI576983
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|29638513|gb|CB643522.1|CB643522
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88353692|gb|CI633083.1|CI633083
EST:     ACACCTCCGAAGTCTACGGCCCCCTCGCAAACGAGATCCTCCTCGGCAAG                         GCGCTGAACCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACAAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88313245|gb|CI594875.1|CI594875
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88301464|gb|CI597157.1|CI597157
EST:     GCACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGAGGGAGCAGGTGCAGGTGGCCAACAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88410056|gb|CI573295.1|CI573295
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|25798009|gb|CA753970.1|CA753970
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88370552|gb|CI590130.1|CI590130
EST:     ACACCTCCGACGTATACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|29682107|gb|CB678382.1|CB678382
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|88359539|gb|CI621070.1|CI621070
EST:     ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 75 (downstream exon)
Score: 28

CGGCGCCGCCGTCATCGCGCACGCCTTCCGCCGCGGCGTCACCTTCTTCGACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcgg ... ggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATTCGGCGGGGCGCCGACGGCGTGCGCGCCGTGTGCGGCCGGCCGGAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGCCGCCGTCATCGCGCACGCCTTCCGCCGCGGCGTCACCTTCTTCGACACCTCCGACGTCTACGGCCCCCTCGCCAACGAGATCCTCCTCGGCAAGgtctggtcggggcccttcccttccttcatcgttcgtggtttcttgtggttggattggatgatgatgagctaaccccatcgccttcggatttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC