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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttctcccctgtgctgttattgaaatatctagcattgttttatccttttacatgatgaactggatttaactgtcttttttttccttttttttttttgcttcatttcttcagCCACACCTGGAAGGTGGCGACAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g48770.1
intron # 3
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|88343864|gb|CI654900.1|CI654900
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88315253|gb|CI611917.1|CI611917
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88722801|gb|CI746311.1|CI746311
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88386212|gb|CI572829.1|CI572829
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88368046|gb|CI572767.1|CI572767
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88312012|gb|CI580177.1|CI580177
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88386211|gb|CI572828.1|CI572828
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACAC-TGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88361848|gb|CI682012.1|CI682012
EST:     GTAACTTCGAGCAAACATACCGTTGTCATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88393733|gb|CI621228.1|CI621228
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|58588357|gb|CF986665.1|CF986665
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCGGTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88738677|gb|CI762185.1|CI762185
EST:     TAACTTTGAGCAAACATACCGGTTGTTATCCAGCATCTTTCTTTGGCAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: TAACTTTGAGCAAACATACCG-TTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88582268|gb|CI699664.1|CI699664
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|58595974|gb|CK006502.1|CK006502
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88359976|gb|CI679746.1|CI679746
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88335570|gb|CI642794.1|CI642794
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88314800|gb|CI608259.1|CI608259
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88349807|gb|CI634342.1|CI634342
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|88330242|gb|CI658551.1|CI658551
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|58689043|gb|CK077730.1|CK077730
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG
EST: gi|14191699|gb|AU183910.1|AU183910
EST:     GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAG                         CCACACCTGGAAGGTGGCGACAAAG
genomic: GTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG

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), 25 (downstream exon)
Score: 10

TTTTATGCAGGATATGGCTACCATGGGAGTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttct ... atttcttcagCCACACCTGGAAGGTGGCGACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactggatttaactgtcttttttttccttttttttttttgcttcatttcttcagCCACACCTGGAAGGTGGCGACAAAG
       atttaac  putative branch site (score: 10)
             ctgtcttttttttcct  CT-rich tract
                tcttttttttcctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttctcccctgtgctgttattgaaatatctagcattgttttatccttttacatgatgaactggatttaactgtcttttttttccttttttttttttgcttcatttcttcagCCACACCTGGAAGGTGGCGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG