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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaacttattgttacttctctaaacaactttacttgagtcatgaag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 5
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaactt--attgttacttctctaaac---------aactttacttgagtcatgaag----------------------------------------------------------------------
||||| ||| |||| ||||||||||||||||||||||||||  | ||||| ||||||||||||||||| ||||| ||||| |||||||  |||| |  || |  | || |  | ||| ||| || |  ||  |    |   |  |||    ||  ||| ||          |||| ||  |  | ||| |                                                                        
GGAAGATACAAAATAATGAGGAATTACATGCCTAAAGTTGGTACCCTTGGCCTTGATATGATGTTCCGGACATGTACTGTGCAGgtgagcatatttctattt--ttatgtgtggattgcattttcagaaatgtcatcactctccatttgagctcatctcaaagatacctgaaactctatctacgacataagttgattcaataaagaagttaactgatttatattatgatagtcttgactgaagttcacacttctatgtccag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G459896_T01 (Zea mays), 5'ss of exon 4
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaactt-attgttacttctctaaacaacttt----acttgagtcatgaag---------------------------------------------------------------------------
||||| |||||||| ||||||||||||||||||||||||||  ||||||  ||||||||||||||||||||||| ||||| |||||||  |||| |  || |  ||    |||| | |||| || |  | |    ||  ||  |||    ||  ||| ||  |        |||  |   ||||                                                                             
GGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTGGTACTCTTGACCTTGATATGATGTTCCGAACATGTACTGTACAGgtgagcatatttctat-ttttatacgtggagtgccatttttagaataacatcactctccatttgagctcatctcaaagatacctggaactctatcaatgacatatgttgattcactaaagaagttaactgatttatattgtgataatcttgactgcagttcacacttctatgtccag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AC183590.4_FGT001 (Zea mays), 5'ss of exon 3
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaacttattgtta---cttctctaaacaacttt--acttgagtcatgaag---------------------------------------------------------------------------
||||| |||||||| |||||||||||||||||||||||| |  ||||||| ||||||||||||||||||||||| ||||| |||||||  |||| |  || |  ||    |||| | |||| || |  | |    ||  ||   | | |   | |||| ||   || |   |||  |  |||||                                                                             
GGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTTGTACTCTTGGCCTTGATATGATGTTCCGAACATGTACTGTGCAGgtgagcatatttctat-ttttatacgtggagtgccatttttagaataacatcactctccgtttgagctcatctcaaagatacctggaactctatccatgacatatgttgattcactaaagaagttaactgatttatattgtgataatcttgactgcagttcacacttctatgtccag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 5
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaaga-aacttgcaaacttattgttacttctctaaacaacttt----acttgagtcatgaag---------------------------------------------------------------------------
||||| |||||||| ||||||||||||||||||||||||||  ||||||| ||||||||||||||||| ||||| ||||| |||||||    || |  || |  || || || | | |||| || |  | ||| | |      |||    ||  ||| ||  |        |||  |   ||||                                                                             
GGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTGGTACTCTTGGCCTTGATATGATGTTCCGGACATGTACTGTGCAGgtgagcgaatttctat-ttttatttgtgaagtgccattttcagaataacatccctctccatttgagctcatctcaaagatacctgaaactctatcgatgaccaaagttgattcactaaagaagttaactgatttatattgtgataatcttgactgaagttcacacttctttgtacag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AC203352.3_FGT001 (Zea mays), 5'ss of exon 2
GGAAGGTACGAAATTATGAGGA------ATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaacttattgttacttc-tctaaacaacttt----acttgagtcatgaag------------------------------------------------------------------------
||||| |||||||| ||||| |       ||||||||||||||||||  | ||||| |||||||||||||||   ||||| ||||| |||||||  |||| |  || |  ||    |||| | |||| || |  | |    ||  ||   | | || || ||| ||  |        |||  |   ||||                                                                          
GGAAGATACGAAATAATGAGCATGTACAGTTACATGCCTAAAGTTGGTACACTTGGCCTTGATATGATGTTCTACACATGTACTGTGCAGgtgagcatatttctat-ttttatgcgtggagtgccatttttagaataacatcactctccatttgacctcatctcaaagatgcctggaactctatcaatgacatatgttgattcactaaagttaactgatttatattgtgataatcttgacttcagttcacacttctatgtccag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 6
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgat-tatatg----ttcatgtactaattttgga-------attccatcttaaagaaacttgcaaa--cttattgtt-----acttctctaaacaactttact--tgagtcatgaag----------------------
||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| ||||||||| | ||||||||||| |||||||  |   ||    ||   |  || |||||  |       |||| |  || || |   |   ||     |||||||     | |  | ||| || || |  |  ||  |  | |                        
GGAAGATACGACATCATGAGGAACTACATGCCTAAAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAGgtgagatgggtgatgatttgcgagctgatttttaacaaagccattctaatttgaacatggtgaaaagagtatattgttgacacaatattataatcagctctcatactggatagtaatatattttatcttaacttttatag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 6
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgttcatgtactaattttggaattccatcttaaagaaacttgcaaacttattgttacttctcta------aacaactttacttgagtcatgaag------------------------------------------------
||||| ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||| | ||||||||||| |||||||  || |||   |||  | |||   || || ||   |||      |  ||||  |||||| | ||    |      ||  | | |  ||  | ||  |                                                  
GGAAGATACGACATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTACAGgtgag-atgtgtgagtgtgatgattcatgatttgcaagctaattt--ttaacaaagctattgtaatttgaacatggtgaaaagagtatctttttgacacaatatataatcagctctcatactggatagtatatatttatcttactttatag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 6
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgt--gatta-tatgttca-tgtactaattttggaattccatcttaaagaaacttgc--------------aaacttattgtta--cttctctaaacaactttacttg-agtcatgaag-
|| || ||||| |||||||| || |||||||| ||||||||  | ||||| |||||||||||| ||||||| || |||||||||||  ||||| |||  | | | | |   ||||   | |     | ||  |||||| |              || |||||| | |  ||| |  ||||  | ||||||| | || |||   
GGGAGATACGACATTATGAGAAACTACATGCCGAAAGTTGGTACCCTTGGTCTTGATATGATGCTCCGAACGTGTACTGTTCAGgttagattaatattctgactttgcgccttttcataatttccttaaactaaactttccagttctcatcaataatcttattttgaaacttatagaaactgcattacttgcaatcttgacag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 6
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtga------ttatatgttcatgtactaattttgg--aattccatcttaaagaaacttgcaaacttattgttacttctctaaacaactttacttgagtcatgaag-----------------------------------------------------------------------------------------
||||| ||||| |||||||||||||||||||| ||||||||||| ||||| ||||||||||||||  ||||||| ||||||||||| |      |  |   ||  ||    ||   ||   |  ||  || ||   || | |  ||   |  | ||  || |  |      | |  |  | || |                                                                                             
GGAAGATACGAGATTATGAGGAATTACATGCCCAAAGTTGGCTCACTTGGACTTGATATGATGTTTAGAACATGTACTGTTCAGgtaagacaaatgctgcatttttggttaaacagtgatcaggtcattcatatcaaacccttgaaggctgattttgttttttcatgattttatcttctattccttggttttgtgaattaccctgcttttaaattgaagtcaataatttatcttctgaatggaaagtgatgatatttctggtttttccttgttgatag

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 5'ss of exon 5
GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatatgtt---------catgtactaattttg---------gaattccatcttaaagaaacttgcaa----acttattgttacttctctaaacaa--ctttacttgagtcatgaag------------------------------------------
|| ||||| || || ||||||||||||||||| |||||||| ||  | || || || ||||||||||| |||||||| |||||||||   ||||            |||  ||  ||  ||         |  ||  || || |  || ||  | |    | ||   |    | ||| | | |   |||| | |     |||  |                                          
GGCAGGTATGAGATAATGAGGAATTACATGCCGAAAGTTGGATCGTTCGGCCTGGACATGATGTTCCGCACATGCACGGTTCAGgtgcgcatataacacctctcgccatagacagatcctgatcacttcagctttttattttgatcaacctgaccacgggatttgccgaatatgctcgatatatttctttgcctccccgatgtggatggtttctcactccgtaactgctgcttaaaatcatgtgcag

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|7219950|gb|AU063307.2|AU063307
EST:     AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAA
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAA
EST: gi|33796283|gb|CF324008.1|CF324008
EST:     AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|55411431|gb|CV723807.1|CV723807
EST:     GTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
genomic: GTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGCACT
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|218498945|gb|FG948066.1|FG948066
EST:     AAGTT-G-TCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCATACT
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|218500233|gb|FG945122.1|FG945122
EST:     TGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTACAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCATACT
genomic: TGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGCACT
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG                         GTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGACATTCCGTACT
genomic: AAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACT

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: 65 (upstream exon), 65 (downstream exon)
Score: 74

GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAGgtgattatat ... agtcatgaagGTTAATCTTGACTTCAGTTCAGAGCAAGATATGATAAGGAAATTCCGTACTGGTCTTGCATTACAACCT




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