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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttctaaccactacttgaatcctttgtgcttatcttttgtttcctgttgtatccttgacactttgttttcttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53700.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 10
-gt-atgcatttctaaccac---tacttgaatcctttgtgcttatcttttgtttcctgttgtatc-------cttgacact-ttgttttcttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
 || || | ||| | | |     ||||| |||     |||  | |  || | || |  ||| |||       ||| | |   |  |||| ||   ||||| |  | ||||| ||||| |||||||||||||||||||| ||||| |||||
tgtgattctttttttatcttacatacttaaatgaaaagtgggtctggttagatttcatttggatctcattttcttaaaataatcatttttttttttgcagATGATTGCATCAGAAGATATAGGGAGGCAGATTTTGACTTATGGAGAAAG
















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|88264876|gb|CI367527.1|CI367527
EST:     GGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88906152|gb|CI375224.1|CI375224
EST:     CAAGTCTGCAGTTTTGATGAACTTGG-ATCCAGA                         GTCGTAGCATCTGAAGACATAGGGA-GCAGATTTTGACGTAT-GGGAAA-
genomic: CAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|89191950|gb|CI250891.1|CI250891
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88838739|gb|CI376277.1|CI376277
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88964180|gb|CI045373.1|CI045373
EST:     TTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGCCAGATTTTGACGTATGGGGAAAG
genomic: TTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|89166280|gb|CI103370.1|CI103370
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88834759|gb|CI370062.1|CI370062
EST:     TTGATGAACTT-GAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: TTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88250927|gb|CI248778.1|CI248778
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|5701695|gb|AU063482.2|AU063482
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|86893269|gb|CI313403.1|CI313403
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATA-GGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|86593940|gb|CI260169.1|CI260169
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|38475250|gb|CF959383.1|CF959383
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|86841142|gb|CI342900.1|CI342900
EST:     CAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: CAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|86434084|gb|CI094427.1|CI094427
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|87021256|gb|CI295315.1|CI295315
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|88967984|gb|CI098226.1|CI098226
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|58597827|gb|CK008355.1|CK008355
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGA                         GTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
genomic: GAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG

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), 75 (downstream exon)
Score: 14

TTACACAAGAACAGCTTGATCGAGCTAAACAGGCAACCAAGTCTGCAGTTTTGATGAACTTGGAATCCAGAgtatgcattt ... ttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttatcttttgtttcctgttgtatccttgacactttgttttcttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG
                           ccttgac  putative branch site (score: 14)
                                   ctttgttttcttcact  CT-rich tract
     tatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatttctaaccactacttgaatcctttgtgcttatcttttgtttcctgttgtatccttgacactttgttttcttcactgcagGTCGTAGCATCTGAAGACATAGGGAGGCAGATTTTGACGTATGGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT