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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctacaatttggatacttctaaaatgatactgagatgaatttagcttgtgttttttcattattacagtttttgacaaaggtcttgtgtgttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATATGTTGTTCAGATGGCAACAATCACAACCAGTCTACAGCCACATCTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g48760.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 3
----ttctacaatttggatacttctaaaatgatactgagatgaatttagcttgtgttttttcattattacagtttttgacaaaggtcttgtgtgttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATATGTTGTTCAGATGGCAACAATCACAACCAGTCTACAGCCACATCTCAAAG
     |   ||   |    |  |   | || | |      ||| ||||| |   | |      |  ||||   |  | | |||     ||       ||| |||||||| |||||||| ||| |||||||  ||| ||||||||||||||| || || |||||||||||||| |||||||| || ||||||||||||||||| |
tcgccttcgcacactat-catgtgctagatcagatgctactgagtttagatgcagatacggtgtctttacc-ctactaataaacac--tgctgaactttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTACGTCGTTCAGATGGCAACGATCACAACTAGCCTACAGCCACATCTCAAGG
















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|88439818|gb|CI541375.1|CI541375
EST:     GCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: GCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88334302|gb|CI642547.1|CI642547
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88555184|gb|CI485426.1|CI485426
EST:     TTGTGGGGAACGCATCCAAG                         GTGAGACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: TTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88349798|gb|CI634333.1|CI634333
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTC
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTC
EST: gi|88491247|gb|CI428519.1|CI428519
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88317589|gb|CI672171.1|CI672171
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAACAGCT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCT
EST: gi|88477298|gb|CI414569.1|CI414569
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88523154|gb|CI450957.1|CI450957
EST:     ACGCATCCAAG                         GTGGAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGGGCTCTCATAT
genomic: ACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88542108|gb|CI471416.1|CI471416
EST:     AACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88458963|gb|CI555644.1|CI555644
EST:     AAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88442145|gb|CI560386.1|CI560386
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88577442|gb|CI674029.1|CI674029
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCA
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCA
EST: gi|88308803|gb|CI654086.1|CI654086
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGA
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGA
EST: gi|25799413|gb|CA755374.1|CA755374
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88210949|gb|CI212589.1|CI212589
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         ATGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88283283|gb|CI404729.1|CI404729
EST:     AAAAGAAAACANTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATA
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAA-Ggtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATA
EST: gi|88524045|gb|CI451929.1|CI451929
EST:     AAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|13165563|gb|AU174360.1|AU174360
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88366550|gb|CI556334.1|CI556334
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|86417819|gb|CI032028.1|CI032028
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCC---                         -----A-AGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88448381|gb|CI555236.1|CI555236
EST:     CTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: CTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88408609|gb|CI686112.1|CI686112
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGT
EST: gi|88514546|gb|CI442052.1|CI442052
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88290434|gb|CI665223.1|CI665223
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTC
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTC
EST: gi|88441599|gb|CI554823.1|CI554823
EST:     AACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88536964|gb|CI464769.1|CI464769
EST:     CTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: CTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
EST: gi|88825494|gb|CI776059.1|CI776059
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGG
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGG
EST: gi|86257033|gb|CI061796.1|CI061796
EST:     AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAG                         GTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT
genomic: AAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATAT

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: 73 (upstream exon), 66 (downstream exon)
Score: 13

AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgt ... ttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATATGTTGTTCAGATGGCAACAATCACAACCAGTCTACAGCCACATCTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgttttttcattattacagtttttgacaaaggtcttgtgtgttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATATGTTGTTCAGATGGCAACAATCACAACCAGTCTACAGCCACATCTCAAAG
                        ttttgac  putative branch site (score: 13)
                                             ttcttgtc  putative PPT
      ttttttcattattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctacaatttggatacttctaaaatgatactgagatgaatttagcttgtgttttttcattattacagtttttgacaaaggtcttgtgtgttcttgtcagGTGAAACAGATCACAAGAGCTTTTCAATTGGTAGATGGGGAGCTCTCATATGTTGTTCAGATGGCAACAATCACAACCAGTCTACAGCCACATCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - gatgaat
- - - - - - - - - - - - - - - - - - - - - - gcttgtg
- - - - - - - - - - - - - - - - - - - - - - -cttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg