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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg...

Basic information

species Oryza sativa
transcript LOC_Os11g08300.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G118800_T01 (Zea mays), 5'ss of exon 3
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagg---gattaattgcaatttttgg
    ||||||| ||| | || || ||||| ||  |||| ||||| ||| | ||||| || ||||| || ||  |||||||||| ||||||||||||||| ||||||| | |      |  | |  |  |  | ||  ||   |    | | |       | || ||   || ||   |      ||||| | ||||    |  
---ATACCTGCGGCCTTAACCACGTTCCCGTCCTCTGCTCAAATCGTGCCGGAGCCCCTCGGTGTGGTGCTCATCATCTCAGCCTGGAACTACCCTTTCAgtaagttgattccaaactgtacgagttctttttgtt-ttttttttctagcttgcccgtctggactatctctgttttttgaatttgattattagcaacagat--

upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 2
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagtt------aaatggtgca---ttcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg
   |||||||| ||| | ||||||||||| ||  | || ||||| ||| | ||||| || || ||||| ||  |||||||||| ||||||||||||||| |||||||      |||  || ||   ||  | | |  | ||  ||  |   ||  |     |||  |      | |        | |||| |   | |           
---GTACCTGCGGCCATAACTACATTCCCGTCCTCCGCCCAAATCGTGCCGGAGCCCCTCGGCGTCGTGCTCATCATCTCAGCCTGGAACTACCCTTTCAgtaagttcattctaaactgtacaatttttttttcttcttcttctagcttgctaggctggactatctctggtttttaattcgaaaaataggaacagaatct---------

upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G26390.1 (Glycine max), 5'ss of exon 3
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa---tggtgcat-tcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatg-ctattgagtagggattaattgcaatttttgg--------
   ||     |  |  || | || || || ||  | ||  |||| || || || || || || || ||  |||||||||| |||||||||||||| ||||||| |||||    | ||   | |  | |  ||||||  | |    | |     | || |||  |     |||  ||    | |    ||||  | |  | | |          
---GTCAAAACTTCAATCGCAACTTTTCCTTCTTCAGCTGAAATAGTATCTGAACCACTGGGGGTTGTGTTAGTCATCTCTGCATGGAACTACCCATTCTgtatgttaatatttagttggtattgtttcacatacttttgagctgacatctcacctttttctttcctccaatctctgcaaaatctatattacattctctgtctatctttccag

upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G24140.1 (Glycine max), 5'ss of exon 3
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa---tggt--gcattcatgtttcatactcgtaattgcata----aacaccgttattccatagagtaatgctat-tgagtagggatta----attgcaatttttgg------------
   ||     |  |  || | || || || ||  | ||  |||| || || || || || || || ||  |||||||||| |||||||||||||| ||||||| |||||    | ||  |||||  | |  ||| ||  | |    | |    | |    |  ||||   |||   ||| |  |   ||  ||| |    ||| || | | |              
---GTCAAAACTTCAATCGCAACTTTTCCTTCTTCAGCTGAAATAGTATCTGAACCACTGGGGGTTGTGTTAGTCATCTCTGCATGGAACTACCCATTCTgtatgttaatatttagtcagcatt-gtctcacatgcttttgagctgacatctcacctttttctttcctccgagctctgcaaaatctataaagatgataatattacattctctatctatctttgcag

upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G44170.3 (Arabidopsis thaliana), 5'ss of exon 3
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg
   | |    |  | || || || || ||  || | ||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||| |||||  ||| |||           | | |||| | |||   | ||  ||    ||  ||  |    || || |  || ||   |     ||  ||||||       
---GCAAAGACTTCTCTAACAACGTTTCCTGCATCCGCGGAGATTGTGTCTGAGCCTCTTGGTGTTGTGCTAGTGATCTCGGCTTGGAACTATCCTTTTCgtatgttccgatcactgattaagtttta-actataagttatat---tacattttgtatgaagtgtgacactttttttt-----ttttttgcaag------

upper sequence: LOC_Os11g08300.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv07s0031g02630.t01 (Vitis vinifera), 5'ss of exon 5
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgcta-ttgagtagggattaattgca-atttttgg
   |      |  |  | || ||||  |||||| | ||| ||||||||||||| ||||||||||||||  | ||||||||| ||||||| || ||||| |||| || |       |  |  | |  || |     |  |  |  || |||  |  |   |||  |  ||| |  |   |  | ||   |   | |  | || 
---GCCAAAACTTCAATGACAACATATCCATCATCAGCAGAAATTGTGTCAGAACCTCTTGGTGTCGTGTTGGTCATCTCAACATGGAATTATCCTTTGTgtatgtaaggcaa--ccctggtatcacacaacttcatatctaggaaaaccaatcatatctagcatgttgcaagctatatttgaatagttcatatagctctga

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|58594363|gb|CF992671.1|CF992671
EST:     TAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATGGAGGCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: TAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88593628|gb|CI713582.1|CI713582
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|33794991|gb|CF323375.1|CF323375
EST:     GCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: GCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58591471|gb|CF989779.1|CF989779
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTGCT                         GGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88669438|gb|CI723356.1|CI723356
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88905564|gb|CI712863.1|CI712863
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88666761|gb|CI718897.1|CI718897
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|58691193|gb|CK079880.1|CK079880
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88594696|gb|CI714654.1|CI714654
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88675380|gb|CI729493.1|CI729493
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
EST: gi|88908685|gb|CI714827.1|CI714827
EST:     AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT                         TGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG
genomic: AGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTG

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), 74 (downstream exon)
Score: 70

CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaa ... tcttttgtagTGCTCTCCATCGACCCAGTCATAGGAGCAATTGCTGCTGGGAATGCCGTTGTGCTGAAGCCATCAGAAATTGCACCAGCCACCTCAGCATTGTTCGCCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCTgtaagttaaatggtgcattcatgtttcatactcgtaattgcataaacaccgttattccatagagtaatgctattgagtagggattaattgcaatttttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA