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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttatttctttctgtttactcattatcaaccgtcttccatagttacaattttgtgaagtttatccatgttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACTTATTACTTAAGGGTAGTTGGATGGAGTTTCACCACTTTTAGCACTCAAC

Basic information

species Oryza sativa
transcript LOC_Os01g11370.1
intron # 23
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|88978651|gb|CI384992.1|CI384992
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88260963|gb|CI364539.1|CI364539
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88256016|gb|CI358404.1|CI358404
EST:     TCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|86872000|gb|CI332172.1|CI332172
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|89177630|gb|CI390809.1|CI390809
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|89177487|gb|CI390666.1|CI390666
EST:     TCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|86851528|gb|CI314111.1|CI314111
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|29658870|gb|CB655145.1|CB655145
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88843542|gb|CI372442.1|CI372442
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88251135|gb|CI349365.1|CI349365
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|86874635|gb|CI318194.1|CI318194
EST:     TTTTTATCAGTTCC-GACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88835112|gb|CI370415.1|CI370415
EST:     TCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|29624814|gb|CB629825.1|CB629825
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88456914|gb|CI529115.1|CI529115
EST:     GTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: GTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|29667511|gb|CB663786.1|CB663786
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|89177631|gb|CI390810.1|CI390810
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTTCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|88376310|gb|CI533212.1|CI533212
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|86880512|gb|CI321001.1|CI321001
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|29625176|gb|CB630187.1|CB630187
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
EST: gi|86893519|gb|CI313518.1|CI313518
EST:     TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATG                         AAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT
genomic: TTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACT

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: 72 (upstream exon), 74 (downstream exon)
Score: 11

CGTAATGTTATTGCCATTGAACCATCATGGCTTACGGAAGCTGCACCACATTTTTATCAGTTCCGGACACCCAATCCTGCCCTTCACTAACTATATGATGgtaattttat ... ttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACTTATTACTTAAGGGTAGTTGGATGGAGTTTCACCACTTTTAGCACTCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaaccgtcttccatagttacaattttgtgaagtttatccatgttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACTTATTACTTAAGGGTAGTTGGATGGAGTTTCACCACTTTTAGCACTCAAC
                                           tgttgat  putative branch site (score: 11)
               atagttacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttatttctttctgtttactcattatcaaccgtcttccatagttacaattttgtgaagtttatccatgttgatcgcagAAAACTGCAACTTGATCTTTGCACCTTTTTGCCCTTTTTGGCTATTCTACTTATTACTTAAGGGTAGTTGGATGGAGTTTCACCACTTTTAGCACTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA