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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgctcaacaacaccagattttctttttccctgtgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG

Basic information

species Oryza sativa
transcript LOC_Os04g45010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024887_T01 (Zea mays), 3'ss of exon 1
---------gtaacgctcaacaaca-ccagattttctttttccctg---tgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
         |     |       || ||| ||    | | | | ||   |||||||        ||    |   |||||      ||   ||||||| |      |  |     |  ||   |     |||||||||||||||| ||||||||||| || || ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||| ||||||
gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaaa------taaaccgtttgatggccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG

upper sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G153268_T01 (Zea mays), 3'ss of exon 1
------------------------gtaacgctcaacaacaccagattttctttttccctgtgggaaatcg--atcgtaactcacatggttaa-----ttgtgatcgcg-cgctgcagaggcacgttgattaacttgtgtgggatct-tagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
                         |  |    || |||    |||    ||| |     |  ||  ||   ||   ||  ||||     ||     || |||   ||  || ||| |   |   ||||    |  |  |    ||  |||||||||||||||| ||||||||||| || || ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||| ||||||
gtacgtgcatatgtcctgatgtccatggcttagaaaaacgatcgatccagtttattatcatccgatctctgcatgcaaaaacacaaaaacaagagctttctgacgacgatgcagcaaaccgagaatgatgcgttaattggccgcctgcagATGTGCAGCTACTCCTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG

upper sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaacgctcaacaacaccagattttctttttccctgtgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggca-cgttgattaacttgtgtgg-gatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
                                            |  || | |||||  |  ||  | |   |     | |        | |    ||| |  | ||||  |||   ||||| ||| ||| || ||||||||||| ||  | ||||||||||| || |||||||| |||||||||||  | || |  |||  ||| || ||    ||||
-----------------------------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG

upper sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
gtaacgctcaacaacaccagattttctttt-tccctgtgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
|||    ||  | |  ||   |||||   | |   | |      | | |      | ||     | | | |   ||     |   |||  |     | |   || |      |   ||||| ||| |||||| |||||||| || ||||||||||||||  | || ||||||||||| ||||||||| | || |  |||  |||||| ||     || 
gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatctacgtaaatttatgagatataacaagtgggttttact---ttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT

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|88398288|gb|CI588176.1|CI588176
EST:     CGTACCAAAAGACCTGCTTCAAGTGCAGCCACTGGAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88427074|gb|CI602035.1|CI602035
EST:     GTACCACAAGACCTGCTTCAAGTGCAGCCACTGCCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: GTACCACAAGACCTGCTTCAAGTGCAGCCACTG-CAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88415936|gb|CI594048.1|CI594048
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88414771|gb|CI604129.1|CI604129
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGGGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88441198|gb|CI602220.1|CI602220
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88370488|gb|CI590066.1|CI590066
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88294792|gb|CI604664.1|CI604664
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
EST: gi|88370129|gb|CI585134.1|CI585134
EST:     CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCG                         ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT
genomic: CGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTT

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: 69 (upstream exon), 43 (downstream exon)
Score: 6

GTGCGACAAGACCGTCCACTTCATCGACCTCCTCACCGCCGACGGCGTCCCGTACCACAAGACCTGCTTCAAGTGCAGCCACTGCAAAGGGATTCTCTCGgtaacgctca ... gggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG
                                gattaac  putative branch site (score: 6)
                              ttgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgctcaacaacaccagattttctttttccctgtgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT