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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctgtgattgcatgagttctgggactgaaagtctctttgtttaacccagaagtgctaagttttatgggcaccatattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 13
gtgagtttctgtgattgcatgagttctgggactgaaagtctctttgtttaacccagaagtgctaagttttatgggcaccatatt-ctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG
||||||||||||||| |  | || | | ||||| |   || |||| || |     ||||  || | | || |       ||||| |||||| |||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||| |||||||||||||||
gtgagtttctgtgatggttt-agctattggactaa---tcactttattcagatatgaagctctgaatattgt-------atattactagGTATGGGAGGCCACTAGTGGAGCTAAGCAATTTACCTTTGAAGGACATGAAGCTCCTGTTTATTCTGTGTGTCCACATTACAAGGAAAATATTCAG

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------------------------------------------------gtgagtttctgtg-attgcatgagttctgggactgaaagtctctttgtttaacccagaagtgctaagttttatgggcac-------catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG
                                                                                                     ||||| |||   ||   | | |   |   || |   | | |     ||| |       | |   ||| |||| |         |||  |  |||| ||||| ||  | |  |||   |||||||  || |||||||| |||||||| ||||| |||||||||||||| ||| |||| || | |||||||
gtgccctcgtatttactattttgtgaccatgtttaatatagaccgtgtctcatgttccagaatactcttgtattgcatgaacagtggtatttgggccttaaagtttttgtatgtttttttaatggagactctaaggctttttccaaataatcttacgtggatctttttcatggaccttcttgtgcatcctgcagGTTTGGGATGCTGCAACAGGACGTAAGCAATACACTTTTGAAGGACATGAAGCACCTGTGTACTCTGTTTGTCCTCATCATAAAGAGAGTATTCAG

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------------------gtgagtttctgtgatt---gcatgagttctgggactgaaagtctctttgt------ttaacccagaagtgctaagttttatgggcac---catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG
                                                                    |||  |||  || |||    |||  | |  | ||    || | |  || |      ||    | | | |   |  ||  | |  |     |||  |  |||| ||||| ||  | |  ||    ||||| | ||| ||||||||||||||||| || || |||||||||||||||||  | ||||| |  ||||||
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG

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|58661057|gb|CK049737.1|CK049737
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|88356140|gb|CI627588.1|CI627588
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|29628402|gb|CB633413.1|CB633413
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|29671653|gb|CB667928.1|CB667928
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|29625346|gb|CB630357.1|CB630357
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAAGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|58667991|gb|CK056677.1|CK056677
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|29622174|gb|CB627185.1|CB627185
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
EST: gi|29631515|gb|CB636524.1|CB636524
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAA-Ggtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGA
EST: gi|163927939|gb|EG712951.1|EG712951
EST:     CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG                         GTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA
genomic: CAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAA

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: 75 (upstream exon), 75 (downstream exon)
Score: 115

ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAGgtgagtttct ... catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagtctctttgtttaacccagaagtgctaagttttatgggcaccatattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG
            gtttaac  putative branch site (score: 115)
                             taagttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttctgtgattgcatgagttctgggactgaaagtctctttgtttaacccagaagtgctaagttttatgggcaccatattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA