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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctgtacctaacgattttgttatgtttagttgatgccttttgatctttttcaaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g59990.2
intron # 2
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|30228671|gb|CB966561.1|CB966561
EST:     CTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: CTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88576762|gb|CI673287.1|CI673287
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88328544|gb|CI676754.1|CI676754
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|218481886|gb|FG948632.1|FG948632
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33806682|gb|CF329222.1|CF329222
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|14981286|gb|BI305964.1|BI305964
EST:     GAAAA-ATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|88404907|gb|CI685341.1|CI685341
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|87018104|gb|CI275918.1|CI275918
EST:     TCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: TCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|163922730|gb|EG712201.1|EG712201
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|33690835|gb|CF319074.1|CF319074
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|58591772|gb|CF990080.1|CF990080
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|163927525|gb|EG709957.1|EG709957
EST:     GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
EST: gi|38480261|gb|CF964350.1|CF964350
EST:     GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA                         GACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT
genomic: GGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTAT

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), 75 (downstream exon)
Score: 194

GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAAgtaagttcct ... ggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG
                         ctttaac  putative branch site (score: 194)
                                      ttttcttg  putative PPT
                        tctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctgtacctaacgattttgttatgtttagttgatgccttttgatctttttcaaaataagatctcaccatgatggtctttaacgtgttgttttcttggttttacagGACTGAACTTTGCCGTTTTAGTGGGCAGAAGATATACCCAGGCAAGGGTATCAGGTTCATTCGTGCTGATTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT