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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagcaacaggaaatactgttcaaatttaccgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG

Basic information

species Oryza sativa
transcript LOC_Os03g52340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 8
-agagcaacaggaaatactgttcaaatttaccgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
  ||  || |    | |    |||   |  |  |||| | |||||   ||||||  | |||  ||  || | |||||   || |        | |  |||| | ||||||||||||||||||||||||||| |  | || |||||||| ||||| ||||| |||||||| |||||||||||||||||| |||||||||| |
atgaaaaatattctaaaaccatcagcataccttttgagttcattttgtatgttta-agtggatatttgtttaacaatacttccttctttgcgactgatcagTTGCAGCTGCAGCGAAATGAGGTCATTGCATTGTTCAATCTTCTGAACAGGCTCTCAGAGTCTGTCAAATTTGTACATGAAAAAGGATCATCAATTGAAG

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 8
agagcaacaggaaatactgttcaa------atttac-cgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
  |    |   ||||| | |  ||      || |||   |||| | |||||   ||||||  | |||  ||  || | |||||    ||||| ||  | || ||||| | ||||||||||||||||||||||||||| |  | || |||||||| ||||| ||||| |||||||| |||||||||||||||||| ||||| | || |
--attggcgaaaaatattctaaaaccatcaatatacattttgatttcattttgtatgttta-agtggatatttgtttaacaata---cttcttggcga-ttgttcagTTGCAGCTGCAGCGAAATGAGGTCATTGCATTGTTCAATCTTCTGAACAGGCTCTCAGAGTCTGTCAAATTTGTACATGAAAAAGGATCATCAGTCGAAG
















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|88539718|gb|CI469698.1|CI469698
EST:     GAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: GAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58593304|gb|CF991612.1|CF991612
EST:     CATTGAAGATTCGTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58606099|gb|CK034132.1|CK034132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCGTTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88485242|gb|CI422513.1|CI422513
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|66920628|gb|CX107476.1|CX107476
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|86500373|gb|CI143006.1|CI143006
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88378826|gb|CI681644.1|CI681644
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCA
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCA
EST: gi|88472627|gb|CI409898.1|CI409898
EST:     CATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|33682548|gb|CF310787.1|CF310787
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGA
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGA
EST: gi|29657857|gb|CB654132.1|CB654132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|29619060|gb|CB624072.1|CB624072
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|27576175|gb|CA998869.1|CA998869
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|33679109|gb|CF307348.1|CF307348
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG

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: 52 (upstream exon), 75 (downstream exon)
Score: 35

TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
                     gtctgac  putative branch site (score: 35)
                                           taaattattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagcaacaggaaatactgttcaaatttaccgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG

- agcaaca
- - - - - - - tactgtt
- - - - - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatg