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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgtatatataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 12
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgta-tatataagtaagtaaactgatgcatg-gttggtgtgc-actgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC
             |   |   || |   | |||   | |||   || | |||| ||  |  || |     | || |||||  |   ||  ||    |   |||||||||||||||  |||| || ||||| ||||| ||||| ||| | ||| |||||||| | ||||||||||||||||||||| |                
-------------gtatgtgtatatatgatgatgataatga--gttatctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCA---------------

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G840582_T03 (Zea mays), 3'ss of exon 12
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgta-tatataagtaagtaaactgatgcatg-gttggtgtgc-actgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACAC-TTTCATGGATCAGTAC
             |   |   || |   | |||   | |||   || | |||| ||  |  || |     | || |||||  |   ||  ||    |   |||||||||||||||  |||| || ||||| ||||| ||||| ||| | ||| |||||||| | ||||||||||||||||||||| | ||||||||| || || 
-------------gtatgtgtatatatgatgatgataatga--gttatctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTTCATGGAGCAATA-

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 13
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgtat-atataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC
               ||   ||||||      ||  ||||    ||| |||    | | || |       | |||| || |    |||  |       ||| |||||||| |||||||| || ||||||||||| || || || ||||| |  ||||||   |||||||||||||||||||||   ||||||  |||||| 
--------------gtaaagaatctg-----ctactactgtttctttcttgctcatctgatctcttcttatgaactcattc-cacttgtggattttgacagTGTGTTCCATCTGAGGACAACAATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTAT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G23310.2 (Arabidopsis thaliana), 3'ss of exon 13
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgtat-atataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC--------------------------------
               ||   ||||||      ||  ||||    ||| |||    | | || |       | |||| || |    |||  |       ||| |||||||| |||||||| || ||||||||||| || || || ||||| |  ||||||   |||||||||||||||||||||   ||||||  ||||||                                 
--------------gtaaagaatctg-----ctactactgtttctttcttgctcatctgatctcttcttatgaactcattc-cacttgtggattttgacagtgtgttccatctgaggacaacaatcctgccagCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGACTCAGTATGATAATAACTTTGGTTATTCGAAAATGTGATT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 13
--gacttgtcttcttgataggaaatctga-aaagatatcactgacgattttttgtgtgtatatataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC
     |        || |   |  | | |   ||| |  |  || |    | | |   | | |||   | |  ||  |  |  |   ||  ||||   |  ||||| |||||| | ||||| |||||| ||||||||||||| ||||||||||| || |||   || |||||||||||||| ||    |||||||| || || 
gaagttctaaagggtgcttttatgtttaatggagagaaaaaagagggaactctataattctgtatttttcaacaacttactataacctttttgtg---tctagGGTCTTCCACTTAAGGACAACCATCTTGCCAGCTGAGGAAGACATGCCTGCAATTATGGAAAGTTTCAAGAAGTTCAATGATGAGTTCATGGAACAATAT

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|29615822|gb|CB620834.1|CB620834
EST:     GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAAG                         GGTGTTCCCACCTGAG-ACGACCATCCTGC
genomic: GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCC-ACCTGAGGACGACCATCCTGC
EST: gi|58589467|gb|CF987775.1|CF987775
EST:     CTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGG                         GGTGTTCCACCTGAGGACGAC-ATCCTGCCAGCTGAGGAGGACATGCCTGC
genomic: CTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGC
EST: gi|33381971|gb|CF197314.1|CF197314
EST:     GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGG                         GGTGTTCCACCTGAGGACGACCATCCTGNNNGCTGAGGAGGACATGCCTGC
genomic: GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGC
EST: gi|33381462|gb|CF196805.1|CF196805
EST:     GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGG                         GGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGANNNNNACATGCCTGC
genomic: GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGC
EST: gi|11442608|gb|BF430511.1|BF430511
EST:     GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAA-GAAGG                         GGTGT-CCACCTGAGGACGACCATCCTGCCAGC
genomic: GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGC
EST: gi|38479882|gb|CF963971.1|CF963971
EST:     GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGG                         GGTGTACCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGACTGC
genomic: GCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGC

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), 71 (downstream exon)
Score: 17

AAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCTTCTTGAAGCAACTGGAATATCCACTGTTCCAGGGTCAGGTTTCGGACAAAAAGAAGGgtaggtgttt ... tgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtgtgtatatataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC
                          aactgat  putative branch site (score: 17)
          tatatataagtaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgtatatataagtaagtaaactgatgcatggttggtgtgcactgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACACTTTCATGGATCAGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - -cttcttg
- - - - - - - ataggaaa
- - - - - - - - - - - - - aaaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgg