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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttc-----catcttagctacc--atggctctgtttactaa-acatgttgcttcaatatttttcag-------------
 || || || || || ||||| |||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||| ||       |     |||| |||      ||   ||| |  |  || |    |  | |||    |||||   | || ||  |                 
TCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTATCCATGATAGTTCCTCAGgttctgtgttccgtacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatattaacatcataacttgtgtttttgcag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagct-----accatggctctgt-ttactaaacatgttgcttcaatatttttcag------------------------------------
 || ||||   | |  |||||  | || ||    ||||| || |||||||||||||||||||| ||||||||||| ||||| || |||||| ||||||||||     |  |    ||| |   | |       |||| |     | ||||    |||  |  |   |   ||  |   | ||   |||                                     
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G08370.1 (Glycine max), 5'ss of exon 1
-CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgc----ttcaatatttttcag-----------------------------------
  || || |   | |  |||||  | || ||    ||||| || ||||| |||||||||||||| ||||||||||| ||||| || |||||  ||||||||||     |  |    ||| |   | ||      ||||  ||   |     | |   |  || |||| |    |   | || | |||                                    
TTCCAAAGGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCGAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATCATTCCTCAggtattaaaattggagtttgacagtcctctggctttagaaactg-gatcacgctccttgtacttgtttccaattatcagatgtctcactagcatctacttacgttgtttcgtattttttgaca

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgct-----tcaatatttttcag
 || || |  ||||| || ||  | || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||  ||||||||||        ||  |||| || | |  | |||||  | |     |   ||| | | | || |   || |     | |  ||||| |||
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgt-----gagttgtatttgaaatgt--ttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag----------
 || || |   | || || || ||||||||    ||||| || |||||||||||||| ||||| ||||||||||||||||| || |||||  | || |||||   |  |      |||   | ||  |     |||  |   || | || | | ||||| ||| |   | |  | |||| |            
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATACCCCAGgtattgctgtcggtgtttttctgttgctattctttaa-tgtaatagatcagatgactaaccat-taattactgttttttacccttgtggacag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag----------
 || || |   | || || || ||||||||    ||||| || |||||||||||||| ||||| ||||||||||||||||| || |||||  |||| |||||   |  |      |||    || ||    ||||   |   || | || | | ||||| ||| |   | |  | |||| |            
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctat--tctttaatgtaatagatcagatgactaaccat-taattaccgttttttacccttgtggacag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ16947 (Selaginella moellendorffii), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag
 || || |   | |  ||||| |  ||||||   ||| |||| || ||||||||||| ||||||||||||||||||||| | || |||||  |||||||||||  |       | || |||  |  |    |||  |   | | |  | | ||| | |                         
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttgg-------cgttccaaaatctt---gtctcggtctcgacg--tttcttttccag------------------------

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ16068 (Selaginella moellendorffii), 5'ss of exon 3
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaatttt--cttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag
 || || |   | |  ||||| |  ||||||   ||| |||| || ||||||||||| ||||||||||||||||||||| | || |||||  |||||||||||  |      | | |    | |     || | |  |  |  |  |  | | |||   |                         
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgtttggcgttccaaaatcttgtctcggtctcgagccaacttttcgggcgtttcttttgcag------------------------

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|58589464|gb|CF987772.1|CF987772
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTC
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTC
EST: gi|58686514|gb|CK075201.1|CK075201
EST:     ACATGGGCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|87032311|gb|CI264092.1|CI264092
EST:     CTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: CTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|25806351|gb|CA762312.1|CA762312
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATGGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86506491|gb|CI149124.1|CI149124
EST:     ACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86854905|gb|CI260973.1|CI260973
EST:     CTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: CTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|33688252|gb|CF316491.1|CF316491
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATAGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|86543296|gb|CI183502.1|CI183502
EST:     AACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: AACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
EST: gi|117242276|gb|CT842928.1|CT842928
EST:     ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAG                         ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG
genomic: ACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG

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: 71 (upstream exon), 49 (downstream exon)
Score: 84

CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagc ... tatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC