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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaagattaaatgtttgatttgatgttaatgaagcaaacaattttaatttttgccatttcgcctttcccctaaaataatttcaacccatgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG

Basic information

species Oryza sativa
transcript LOC_Os11g41900.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g41900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 1
---------gctta-agattaaatgtttgatttgatgttaatgaagcaaacaattttaatttttgccatttcgcctttcccctaaaataatttcaacccatgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
         || || |   |  ||||||| | || |||| |||||||||||| |     ||||| || |  ||        | | ||||| |||| |  ||||||||||| ||||||||||||| ||||| ||||||||||   ||||||
aagcacttagcatacacgctttatgtttg-tgtggtgtttatgaagcaaacatt----gttttttccctcccggt-----gccagaataacttcagcttatgttctgcagGTACAACTGCATGCAGATGAGGAAACTTACAGATCAATGG
















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|29658270|gb|CB654545.1|CB654545
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|58680428|gb|CK069115.1|CK069115
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGGGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|88263764|gb|CI366665.1|CI366665
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|117217204|gb|CT845404.1|CT845404
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGGGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|29639076|gb|CB644085.1|CB644085
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|29680413|gb|CB676688.1|CB676688
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|58683813|gb|CK072500.1|CK072500
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGGGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|29639118|gb|CB644127.1|CB644127
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|112785295|gb|EE590405.1|EE590405
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|29615789|gb|CB620801.1|CB620801
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGGGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|4714815|gb|AU055932.1|AU055932
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|58669640|gb|CK058326.1|CK058326
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGGGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
EST: gi|29686573|gb|CB682848.1|CB682848
EST:     TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAG                         ATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
genomic: TGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG

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: 74 (upstream exon), 73 (downstream exon)
Score: 115

GCCGTTCTCGAAGAGCTTGTACCGGCGGATCAACAGGTTCTTGGCCGAGCTGCTGTGGCTTCAGCTGGTCTGGCTTGTGGATTGGTGGGCAGGAGTTAAGgtatgttgat ... tgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttttgccatttcgcctttcccctaaaataatttcaacccatgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG
                        ccctaaa  putative branch site (score: 115)
                           taaaataatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaagattaaatgtttgatttgatgttaatgaagcaaacaattttaatttttgccatttcgcctttcccctaaaataatttcaacccatgttctgcagATACAACTGCATGCTGATGACGAAACTTACAAGGCAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - -tgtttga
- - - - - - - - - - -ttgatgt
- - - - - - - - - - - - - - - -tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa