Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttcttgcttgaatttagactctactataccgccaaagtagtttgtattttgttttgaggggataaccaatctgcttgtactctatggcag

Basic information

species Oryza sativa
transcript LOC_Os01g15310.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G038606_T01 (Zea mays), 5'ss of exon 6
---CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttcttgcttgaatttagactctactataccgccaaagtagtttgtattttgttttgagggg-ataaccaatctgct---tgtactctatggcag
   |||||||||||||||||||| |||||||| |||||||| || ||   |||| ||||||||||||||||||| ||| |||| |  |||||||| | ||||||||  |   | |     | ||| |      || |   |||    |         | ||||  ||||  |  |||||||||      |   |   ||  ||
AAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG---AGGCAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacacttcgtaaccacttacatatatttacagtcccacccca---------tagtttcaagggataccaccaatctgtgggacgcgttacttgttag

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G038606_T02 (Zea mays), 5'ss of exon 6
---CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttcttgcttgaatttagactctactataccgccaaagtagtttgtattttgttttgagggg-ataaccaatctgct---tgtactctatggcag-----
   |||||||||||||||||||| |||||||| |||||||| || ||   |||| ||||||||||||||||||| ||| |||| |  |||||||| | ||||||||  |   | |     | ||| |      || |   |||    |         | ||||  ||||  |  |||||||||      |   |   ||  ||     
AAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG---AGGCAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacacttcgtaaccacttacatatatttacagtcccacccca---------tagtttcaagggataccaccaatctgtgggacgcgttacttgttagtgcag

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G095114_T01 (Zea mays), 5'ss of exon 6
---CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgta--tgcttcttgcttgaatttagac-tctactat--accgccaaagtagtttgtattttgttttgaggggataaccaatctgcttgtactctatggcag
   ||||||||||||||||| || |||||||| |||||||| || ||   |||| |||||||||| |||||||| ||| |||| |  |||||||| | ||||||||  ||||| |||       ||| || |||  | |  |   ||| |     ||  |  |  |    |   |        | | |||||    |   ||||
AAACCTGGAGGCAGAGGCATCGGACGTGGCCAAGATGATGGAGGTAG---AGGCAGTGGTGGCCGAGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacatgctttttgtaaccgcttacacatcttttgttgagtcccacacccaatttcaagtgataccaatctgtgggatgctttacttgt----tggtgcag

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|88848532|gb|CI087054.1|CI087054
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88474998|gb|CI412269.1|CI412269
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88483872|gb|CI421143.1|CI421143
EST:     CGGTGGTGNCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGNTGAGAGGGGAAAGGTTCACTTGTGGGAATGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGA-GGG-AAGG-TCACTTGTGGGAATGC
EST: gi|88214587|gb|CI214436.1|CI214436
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88475016|gb|CI412287.1|CI412287
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCNCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|86504317|gb|CI146950.1|CI146950
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88478076|gb|CI415347.1|CI415347
EST:     GGT-GTNGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: GGTGGT-GGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88558601|gb|CI489101.1|CI489101
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88531457|gb|CI459934.1|CI459934
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88202538|gb|CI200893.1|CI200893
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88471544|gb|CI408815.1|CI408815
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88542529|gb|CI471864.1|CI471864
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88474997|gb|CI412268.1|CI412268
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88979842|gb|CI026148.1|CI026148
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|89199230|gb|CI255496.1|CI255496
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGNCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88548229|gb|CI476582.1|CI476582
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88554684|gb|CI484877.1|CI484877
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88208022|gb|CI207871.1|CI207871
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGGAAG-TCACTTGTGGGAATGCCG
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGG-AAGGTCACTTGTGGGAATGCCG
EST: gi|86509038|gb|CI151671.1|CI151671
EST:     CGTTGGTGTCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGTCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88241907|gb|CI241756.1|CI241756
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88214580|gb|CI214429.1|CI214429
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|3761805|gb|C99053.1|C99053
EST:     CGGTGGTGNCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|89170615|gb|CI039892.1|CI039892
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|3761804|gb|C99052.1|C99052
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGAC-TGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88241526|gb|CI241375.1|CI241375
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|87025899|gb|CI282476.1|CI282476
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|88483094|gb|CI420365.1|CI420365
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
EST: gi|89193834|gb|CI018152.1|CI018152
EST:     CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAG                         GTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC
genomic: CGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGC

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: 42 (upstream exon), 56 (downstream exon)
Score: 5

CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttct ... tctatggcagGTGGGGGCCGCGGACGTGGGTGAGAGGGAAGGTCACTTGTGGGAATGCCGCTTTTTTAAGGCTTTGTGTCACATAGATTGCTTTAGGAGGGTGAAGAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttcttgcttgaatttagactctactataccgccaaagtagtttgtattttgttttgaggggataaccaatctgcttgtactctatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG