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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g56630.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgtttt-cagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                               | |||||       ||| ||  ||| |||         | | |||   |   || |||||||||      |||||| ||     ||||| ||   |||  | |||| ||||||||||| ||||| ||||||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| ||||| ||
----------------------------atctaaaatga----attttaatt-ttggacagagggagtatttatgatggc---aagatattctggcaataagattgactg-----acaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 15
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatg-atctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                            |   ||  |     |||||| |    ||  | |    || |   || |  |    ||  | ||||||       ||||  ||     |||||||| |||  ||   ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||| || |||||||||||||||||| ||||||||||||| ||
----------------------------gtagtagtttcatcttcttttacttctgggcttaaatttatgtatttatgatggcaaggtcttctggcaataatattggctg-----acaatatacaattcattatttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAGTTCTTCATCCCATATGCATGGCGCCTTGTCCTATCACGGGG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 15
gtgatgcttataatacttagaaactgctgctttaaatggcagt-tctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgttt-tcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                               | | |||| | | | |||  |||||     ||| |||    | ||          ||||   |   ||     |||  | | ||   |  |     |    ||||| |||||||||||| ||  | || || |||||||| ||||| |||||||| ||||||||||||||||||||||  ||||   | || ||||| ||  |
------------------------------gtaagatggaaatatattttttgatttgtggtttgcttccagtgtgg---------aataccattaggtggattttgtcttgtttc-tatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 15
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgtttt----cagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                                         ||    |||  |||     | ||| || | |     || | |  ||||   |   |   |||||   || ||      || |  |  || | || |    ||||||||||| ||  | |  || |||||||| ||||| ||||| || ||||||||||||||||||||||  ||||   | || |||||  || |
-----------------------------------------gtaaaatgaaaatttgtgttattcgtgctttacacccaataggtaataacattagg--aggattacctgtctcacttctacaagactatatcttgtttggcagATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 14
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaa----atattctggtgtccggattgattggcttgacaatatataatgat---ctgttt-tcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                                             |  ||||     | ||||| |  ||  | |    |||  |       || |   |    |||||  ||| |||     |||       |    ||||| |||||||||||| ||  | || || |||||||| ||||| |||||||| ||||||||||||||||||||||  ||||   | || ||||| |   |
--------------------------------------------gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattatttgtcttatttctatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 15
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggt--gtccggattgattggcttgacaatatataatgatctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                                |||| |||| ||  ||| |||  |||  |    ||||||    |     ||||  |  ||||    ||   | |  | |        |||||| |||   |  ||  ||||||||||| || ||||| || |||||||| ||||| || ||||| |||||||| |||||||| ||||  ||||   | || ||||| ||  |
-------------------------------gtaaaaggcaattggttgttga--gcaattacagttgttcc---aattaatgaatcttatctgaaaggttatgttccacttatcacgtaatata-aatttccgtttgacagATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG

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|33683149|gb|CF311388.1|CF311388
EST:     TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
genomic: TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
EST: gi|5004229|gb|AU069378.1|AU069378
EST:     TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
genomic: TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
EST: gi|89167227|gb|CI104513.1|CI104513
EST:     TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
genomic: TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
EST: gi|33800537|gb|CF326139.1|CF326139
EST:     CTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
genomic: CTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
EST: gi|5004218|gb|AU069367.1|AU069367
EST:     TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
genomic: TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAG
EST: gi|86497820|gb|CI140453.1|CI140453
EST:     TTGAGGTTATTAACCAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAG                         ATGTTTACCCAGTTACGGTTTACATATGAGCCAAGAAAGTCATCCTGAGGA
genomic: TTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAG-CAAGAAAGTCATCCTGAGGA

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: 46 (upstream exon), 73 (downstream exon)
Score: 13

TCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCATGGCGTGGAGAAGGAATGAAGgtgatgctta ... ctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattctggtgtccggattgattggcttgacaatatataatgatctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG
                         gcttgac  putative branch site (score: 13)
                                            tctgttttc  putative PPT
                           ttgacaatatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgttttcagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG