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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgctgtgtttacacaatcttaattcagagtacagcttcacttctcattgatcagtgtttaaacaatgaaatcatatttttctctttatcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG

Basic information

species Oryza sativa
transcript LOC_Os02g02560.1
intron # 18
splice site 3'
intron type U2

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|88250631|gb|CI348861.1|CI348861
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86835725|gb|CI348182.1|CI348182
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86836204|gb|CI346206.1|CI346206
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|87032112|gb|CI362192.1|CI362192
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86601109|gb|CI356866.1|CI356866
EST:     CCTTGAAGGTTTCCGGTGATGTTTGTTTTGGCTCTAGCATCACATTGAAG                         GGCAA-GTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86595013|gb|CI258267.1|CI258267
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|7332555|gb|AU085901.1|AU085901
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88258425|gb|CI361011.1|CI361011
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAA-                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86839753|gb|CI343676.1|CI343676
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88261397|gb|CI364973.1|CI364973
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88261483|gb|CI365059.1|CI365059
EST:     CCTTGAAGGTTTCCCGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86835715|gb|CI348172.1|CI348172
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88260254|gb|CI362547.1|CI362547
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86479595|gb|CI122228.1|CI122228
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88261093|gb|CI364669.1|CI364669
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88256960|gb|CI359348.1|CI359348
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|66947245|gb|AU312089.1|AU312089
EST:     CTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86859745|gb|CI345407.1|CI345407
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86834286|gb|CI344046.1|CI344046
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88252508|gb|CI350936.1|CI350936
EST:     TCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: TCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86598561|gb|CI355178.1|CI355178
EST:     TGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: TGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|66922584|gb|CX109432.1|CX109432
EST:     CTTGAAGGTTTCCGGTGATGTATGGTTAGGCTCTAGCATCACCATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCCAG
genomic: CTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCAC-ATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCC-AG
EST: gi|86841180|gb|CI342925.1|CI342925
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88994067|gb|CI116031.1|CI116031
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|86823815|gb|CI258831.1|CI258831
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
EST: gi|88254412|gb|CI353236.1|CI353236
EST:     CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAG                         GGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT
genomic: CCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGAT

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: 64 (upstream exon), 12 (downstream exon)
Score: 1

GTGTTTCCTTGGTCGCTTCAAGTCAATCCCCAGCATTGTTGAGCTTGACACCTTGAAGGTTTCCGGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGgtacttttgc ... tcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattgatcagtgtttaaacaatgaaatcatatttttctctttatcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG
  cattgat  putative branch site (score: 1)
                            tcatatttttctcttt  putative PPT
                         aaatcatatttttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgctgtgtttacacaatcttaattcagagtacagcttcacttctcattgatcagtgtttaaacaatgaaatcatatttttctctttatcttttaaagGGCAAGGTGACCATCACAGCCCAACCTGGTGTCAAACTGGAAATCCCAGATGGAGCAGTGATCGAGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
-tatgctg
- - - - - - -acacaat
- - - - - - - - - - - - - - - - - - gcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaacaa