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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttactcaaatgttgattggtaatttgttttactctcagcaccctttcctcagaacttgatgatcattcttatgatattttttttcttctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAATTTCTGGAGGATGATTTGCCCGATAGTCCTGATGCACTCGACCTCCAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g56200.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56200.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G076450_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------------tatttactcaaatgttgattggtaatttgttttactctcagcaccctttcctcagaacttgatgatcattcttatgatattttttttcttctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAATTTCTGGAGGATGATTTGCCCGATAGTCCTGATGCACTCGACCTCCAAAA
                                                                                               | |||   || ||  ||||  | | ||||  |    ||  |    | |     | ||         |||      | || |       ||  || |||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| || |||||||| ||| |||| ||  |||  ||     || ||||||| | 
gtgaaagtttcaaccgtcaaccttttccattgtagtgaacatgccctgcagctatctccagaaaatttagttcggacgcaatcacggattctacgtgtacctgaa-gt--attgtgactatgttcaaaatacatgattgatacaatgtatctgatctggtgttcgcccatttttatccgatgacttcttgcagTGGAGCTGGGCCGTCGGTACTTCCCGAACTGCTCGCAGGTGCTGGACAAGTTCCTGGAGGACGATCTGCCGGAAGGTCTGGACCAGTTCTACCTCCAGAG
















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|88235674|gb|CI234876.1|CI234876
EST:     AACACAAAACAAGAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|29630864|gb|CB635873.1|CB635873
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|88249958|gb|CI249807.1|CI249807
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|58668997|gb|CK057683.1|CK057683
EST:     ACACAAAACAAAAGGCTCCGTTCAAGGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: ACACAAAACAAAAGGCTCCGTTCAA-GGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|86429043|gb|CI075724.1|CI075724
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|58594357|gb|CF992665.1|CF992665
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|87041286|gb|CI195908.1|CI195908
EST:     CAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTTAACTGCTCGCAGGTGCTCGACAAA
genomic: CAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCC-TAACTGCTCGCAGGTGCTCGACAAA
EST: gi|88288804|gb|CI517935.1|CI517935
EST:     AACACAANACCAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|86831647|gb|CI301497.1|CI301497
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|218501333|gb|FG958583.1|FG958583
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|87041405|gb|CI196027.1|CI196027
EST:     ACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: ACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
EST: gi|29628520|gb|CB633531.1|CB633531
EST:     AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAG                         TTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT
genomic: AACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAAT

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), 73 (downstream exon)
Score: 37

GCTAGCACTTCTGGAAAATTGAAGGAAGTCGATCTGAACGAGACACCAGTAACACAAAACAAAAGGCTCCGTTCAAGGGTGGATGCACTCATGAAAACAGgtcggaactg ... ctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAATTTCTGGAGGATGATTTGCCCGATAGTCCTGATGCACTCGACCTCCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcctcagaacttgatgatcattcttatgatattttttttcttctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAATTTCTGGAGGATGATTTGCCCGATAGTCCTGATGCACTCGACCTCCAAAA
           acttgat  putative branch site (score: 37)
                                tattttttttcttctg  putative PPT
                   atcattcttatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttactcaaatgttgattggtaatttgttttactctcagcaccctttcctcagaacttgatgatcattcttatgatattttttttcttctgttttcagTTGAGCTGGGACGTCGCTACTTCCCTAACTGCTCGCAGGTGCTCGACAAATTTCTGGAGGATGATTTGCCCGATAGTCCTGATGCACTCGACCTCCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - -atgttga
- - - - - - - - - - - - - - - - - - - cagcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatga