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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttgattttgctgttgtattgctattctatcatcttccaactgatgcatacctagcatgagtttgaactgttgtaagctgccttagttttttag...

Basic information

species Oryza sativa
transcript LOC_Os11g29380.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 16
GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttgattttgctgttgtattgctattctatcatct--tccaactgatgcatacctagcatgagtttgaactgttgtaagctgccttagttttttag-
|||||||||||||||||||||||| |||||||| ||||| ||| |||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||||| |||||   ||| |||||   || ||||  ||||||   | | ||  | | | |   |           |  |  |||||     || |    ||||  
GAGCTACGTGTCTCAGGAAGATGTTGACATGGCCATCCGTGTCTTGCTTGACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg---ttggtgttgagctgttattacatcatccagtgctacacaagtacatgcacttgataaacaatttaatgtaaaagtgctcatccatttaac

upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 15
GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttgat--tttgctgttgtattgctattctatcatcttccaactgatgcatacc--tagcatgagtttgaactgttgtaagctgccttagttttttag
|    | ||  | || || ||||| |||||||| || || || || ||||| ||||| ||||||||||| || ||||| || ||||| || |||||||||||| ||    ||  | ||   |||       ||||| | |  | |  | |  | |||  |   |   |  |||  || | || | |  |     | ||||||  
GCAACATGTTACACAAGAGGATGTGGACATGGCAATTCGTGTTCTTCTTGAATCATTCATTTCAACTCAAAAATTTGGGGTGCAGAAGGCTCTTCAAAAGgtatataaaaatattctgaatttgccacataattctgttaaatgctga-tattccatggcatcatattttgttcaaattattttta-ttttggcattttttt--

upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 15
GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgta----aattttgattttgctgttgtattgctattctatcatcttccaactgatgcatacctagcatgagtttgaactgttgtaagctgccttagttttttag
     | ||  | ||||||||||| ||||||||||| || ||||||||||| || || |||||||| || || || || || |||||||| || |||||||||    ||   |   |||||  ||| ||| ||   | ||  | || |   |     |||      |||  | |  | || |   | |      | |   |   
ACAGCATGTTACCCAGGAAGATGTTGACATGGCTATTCGTGTCCTGCTTGATTCTTTCATTTCAACACAAAAATTCGGGGTGCAGAAAGCCCTACAAAAGgtactgaaaagatatatttgcctttgcattccttaaccattctttttctcttagaatatattctatatgtttgtccaatgatcctatc-attggaatcaat---

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|86597612|gb|CI274603.1|CI274603
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87016236|gb|CI271647.1|CI271647
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86429086|gb|CI075767.1|CI075767
EST:     TTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: TTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86437499|gb|CI119221.1|CI119221
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86482314|gb|CI124947.1|CI124947
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|88845092|gb|CI084017.1|CI084017
EST:     GTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGGAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: GTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86480334|gb|CI122967.1|CI122967
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86437458|gb|CI119180.1|CI119180
EST:     ACTCATTTATTTCAACTCGGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87023311|gb|CI272139.1|CI272139
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         GATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87032692|gb|CI270327.1|CI270327
EST:     CATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: CATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86436900|gb|CI118622.1|CI118622
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|88244982|gb|CI244831.1|CI244831
EST:     ATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86493580|gb|CI136213.1|CI136213
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86437708|gb|CI119628.1|CI119628
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86597015|gb|CI272610.1|CI272610
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86481049|gb|CI123682.1|CI123682
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCGCTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87017949|gb|CI273971.1|CI273971
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|88831233|gb|CI082043.1|CI082043
EST:     ATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87031839|gb|CI272540.1|CI272540
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|29630148|gb|CB635157.1|CB635157
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|87021134|gb|CI271941.1|CI271941
EST:     ACTCATTTATTTCAACTCAGGGGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
EST: gi|86518590|gb|CI158796.1|CI158796
EST:     ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAG                         AATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG
genomic: ACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTG

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: 68 (upstream exon), 58 (downstream exon)
Score: 16

GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttg ... gcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTGCTTCTTCTGCGCACCCTGGTCAAGGATGTGCTGCACTTCGAAGAAATCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTACGTGTCTCAGGAAGATGTCGACATGGCTATCCGCGTCCTGCTTGACTCATTTATTTCAACTCAGAAGTTTGGTGTACAGAAAGCACTTCAAAAGgtaaattttgattttgctgttgtattgctattctatcatcttccaactgatgcatacctagcatgagtttgaactgttgtaagctgccttagttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT