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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatactaccgtctaataataatcggtcaatgtcattttgcgatttgggtgctgtgattttgatatcatattttggtcaagtagaacgtggcgc...

Basic information

species Oryza sativa
transcript LOC_Os08g31830.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G062289_T01 (Zea mays), 5'ss of exon 1
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatact-accgtctaataataatcggtcaatgtcattttgcgatttgggtgctgtgattttgatatcatattttggtcaagtagaacgtggcgc
   |||||||||||||   ||  |||||  |||||||||||||||||||| |||||||||||||||||| || ||||| ||||||||||||||| ||||||||||    | |  | | |          |    |||     |        |||  |      |       | |||| |||   ||| || | ||  ||  
CCCCATGGCGACGGCGCTCAAATCGTTCCTGAACAGCCCCGTCGGCCCCAAGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctctgcggatcatgcttgggctcttacgcaaacctgtgcgattcgttgacttaaacaacgcgccgaacatagtttca-caattatatcgatgctg

upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G139805_T01 (Zea mays), 5'ss of exon 2
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatac--taccgtctaataataatcggtcaatgtcattttg--cgatttgggtgctgtgattttg---atatcatattttggtcaagtagaacgtggcgc
   ||||||||| |||   ||| |||||| |||||||||||| ||||||| |||||||||||||||||| || || || ||||||||||||||| ||||||||||    | |  | |   ||     |  |  |   | |  | | ||  ||||| | |  ||   |    |     | | || |||   ||| || |         
CCTCATGGCGACCGCGCTCAAGTCGTTCTTGAACAGCCCCGTTGGCCCCAAGACCACCCACTTCTGGGGCCCTGTTGCCAACTGGGGCTTCGTCGTCGCGgtacgcctctgcagttcatgcttgggttcttacgcttacgcaaatctgtgcgattcgcggacttcaacaacgcacgcaacgtaatttttgcaattatatt-------

upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP07373 (Chlamydomonas reinhardtii), 5'ss of exon 1
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgta---cgaacatactaccgtctaataataatcggtcaatgtcattttgcgatttg-ggtgctgtgattttgatatcatattttggtcaag-tagaacgtgg-cgc--------------------------
   ||||||| |       | |  ||    |||   |||   ||| || | ||| || || || ||||| || |||||||||||||||||||| |||||||||   ||    ||||   | |   |  |  |  |  |||| | |  |    || | |  | |         | |  |    || |||  | | || | ||| |||                          
CTCCATGGCGTCTCGATTTATGCAGTGGGTGAATTCCCCAACCGGTCCAAAGACAACTCATTTTTGGGGGCCAGTCGCTAACTGGGGCTTCGTGCTCGCGgtaggtcggcagtacttgggccctgtggtctttcggaaatgacttactcatgttagtgacggttaaggcgccacaaaacggcttcgtctggctcgatcatggacgcctgacccatcatcctacgcgctgcag

upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S31_282V6.1 (Physcomitrella patens), 5'ss of exon 2
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatactaccg-tctaataataatcggtcaatgtcattttgcgatttgggtgctgtgattttgatatcatattttggtcaagtagaacgtggcgc
 |       | |||||  |   || ||||||||||| ||||| || || | ||| || |||||||||||||| || || |||||||| ||||| || |||||||  || | || |   ||||  |  ||  |||     | | ||   |     |  |||||||||| |   |     |  |    |     |   |  | 
CGCTGCCATGGCGGCGATGCGTGCATTCTGGAACAGTCCCGTGGGGCCGAAGACTACGCACTTCTGGGGTCCAGTGGCGAACTGGGGTTTCGTACTTGCGgtactgacctccttcttctctatcacgaagtggttcgactgacttgctgtgaatgcggctgtgatttggggttgtggatgggactgaagctcatacgaag-

upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ19442 (Selaginella moellendorffii), 5'ss of exon 1
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatactaccgtctaataataatcggtcaatgtcattttgcgatttgggtgctgtgattttgatatcatattttggtcaagtagaacgtggcgc
                   |||  | |||||||||||   |||||||||| ||| || || |||||||||||| |||| || ||||||||||||   || ||  |   ||     |  |||     | ||  || | ||  ||  |  |||      | | ||||  |  |||  |                        
----------------CTCAAGAAGATCTGGAACAGCGAGGTCGGCCCCAAGACGACGCATTTCTGGGGTCCCATCGCGAATTGGGGCTTCGTCGCGGCTgtgagtggatttcttctcctag----attc--tcgaggtttttggggaattgcttctcagagattgcgcaatcgcag-----------------------

upper sequence: LOC_Os08g31830.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ21059 (Selaginella moellendorffii), 5'ss of exon 1
GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacatactaccgtctaataataatcggtcaatgtcattttgcgatttgggtgctgtgattttgatatcatattttggtcaagtagaacgtggcgc
                   |||  | |||||||||||   |||||||||| ||| || || |||||||||||| |||| || ||||||||||||   || ||  |   ||     |  |||     | ||  || | ||  ||  |  |||      | | ||||  |  |||  |                        
----------------CTCAAGAAGATCTGGAACAGCGAGGTCGGCCCCAAGACGACGCATTTCTGGGGTCCCATCGCGAATTGGGGCTTCGTCGCGGCTgtgagtggatttcttctcctag----attc--tcgaggtttttggggaattgcttctcagggattgcgcaatcgcag-----------------------

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|33821443|gb|CF336533.1|CF336533
EST:     GTCCCGTCGCTAACTGGGGCTTCGTCCTCGCG                         GGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
genomic: GTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacat ... tttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
EST: gi|33659948|gb|CF290915.1|CF290915
EST:     GGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCG                         GGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
genomic: GGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacat ... tttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
EST: gi|88983378|gb|CI028614.1|CI028614
EST:     GGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCG                         GGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
genomic: GGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacat ... tttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACA
EST: gi|427741|gb|D23876.1|D23876
EST:     GGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCG                         GGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCCGGCAATATGAC
genomic: GGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacat ... tttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCC-GGCAATATGAC

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: 73 (upstream exon), 55 (downstream exon)
Score: 11

GGGCATGGCGACGGCGGCGAAGGCGTTCTGGAACAGCCCCGTCGGCCCCAGGACCACCCACTTCTGGGGTCCCGTCGCTAACTGGGGCTTCGTCCTCGCGgtacgaacat ... tttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACAGCAG




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