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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCGGCGGCGACGGCGAGATGGTGCAGCGCCTGACGTACCGCAAAAGGCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatcttctctcttcttggggcactttttcttttggggttgggttcttgatctgttgaggtggaagatttttcgcctggttgagcgagcttttgtggcgttgtggttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g24690.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G166963_T02 (Zea mays), 5'ss of exon 1
GGCGGCGGCGGCGACGGCGAGATGGTGCAGCGCCTGACGTACCGCAAAAGGCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatcttctct-cttcttggggcactttttcttttggggttgggttcttgatctgttgaggtggaagatttttcgcctggttgagcgagcttttgtggcgttgtggttgcag---------
||||   ||| || |||| ||||||||||||| ||||| ||||||||  |||||||||||||||||||||| || |||||||||||||||||||| || |||| |||||| |||  |||| |    || ||| |||| ||   ||   ||     | |||||        ||| | | |   | |||||   | ||||   | | |    | |            
GGCGCGCGCGACGGCGGCAAGATGGTGCAGCGTCTGACCTACCGCAAGCGGCACAGCTATGCCACGAAGTCCAACCAGACGCGGGTCGTCAAGACCCCTGgtccggatctcctcgacttcctat--cattttctcttctgt--ttccttttcacttttgttggttcctttgatatcttg---gtttgagtatgttttttatgtgctagattggtttgtttttcag

upper sequence: LOC_Os09g24690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G05740.1 (Glycine max), 5'ss of exon 1
-GGCG-GCGGCGGCGACGGCGAGATGGTGCAGCGCCTGACGTACCGCAAAAGGCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgt--ctggatcttctctcttcttggggcactttttct--------tttggggttgggttcttgatctgttgaggtggaagatttttcgcc------tggttgagcgag------cttttgtggcgttgtggttgcag-----
  ||| |   |   ||||   ||||||||||||| || || ||||||||  |||||||||||||||| ||||| || ||     |||||||||| || || |||      |||    |    ||       |||    |        |||  | ||  ||| ||| | ||||       || | |||| |        |||||  ||  |      ||| | |||   |||||    |      
GAGCGTGATCCATTGACGA--AGATGGTGCAGCGTCTCACCTACCGCAAGCGGCACAGCTATGCCACCAAGTCCAACCAACACAGGGTCGTCAAAACCCCTGgtaatcaaatccctccctcactgattatgcttcggatcggaacaatttttgtttttgtttttgttttgttttaaaaaaaaagtttttggtattaattggttctgctgggtacgtcttgtttggttctgtgggaataatgcag

upper sequence: LOC_Os09g24690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G11920.1 (Glycine max), 5'ss of exon 1
-GGCG-GCGGCGGCGACGGCGAGATGGTGCAGCGCCTGACGTACCGCAAAAGGCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatcttctctcttcttggggcacttt--ttcttttggggttgggttcttgatctgttgaggtggaagatttttcgcctggttg--agcgagcttttgtgg---cgttgtggttgcag-----------------
  ||| |   |   ||||   ||||||||||||| || || |||||||| ||||||||||||||||| || || || ||     |||||||||| || || |||    |||   || ||  | ||  | | |   |   | |  | ||  | |    ||| |   |  |      ||||     ||| |   |    | | |   ||    |||||| |||  |                 
GAGCGTGATCCATTGACGA--AGATGGTGCAGCGTCTCACCTACCGCAAGAGGCACAGCTATGCCACCAAATCCAACCAACACAGGGTCGTCAAAACCCCTGgt---aatcaaatccctcttcggaacccctcactcactcttcgattatgcttcgaatcggaacaatttttgctttttaattttgggtattaattggttctgacgggtatgttgtgtttggtgatgtgggaataatgcag

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|88975429|gb|CI023680.1|CI023680
EST:     GGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88961791|gb|CI096951.1|CI096951
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|27576721|gb|CA999415.1|CA999415
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88212826|gb|CI210677.1|CI210677
EST:     CACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: CACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|86596546|gb|CI284857.1|CI284857
EST:     AATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: AATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|58668332|gb|CK057018.1|CK057018
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGACCAAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|86257931|gb|CI064284.1|CI064284
EST:     CACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: CACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|87033868|gb|CI188492.1|CI188492
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAAGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|86533492|gb|CI173698.1|CI173698
EST:     ACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCGG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: ACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88209963|gb|CI209812.1|CI209812
EST:     GTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|87032333|gb|CI264114.1|CI264114
EST:     CCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: CCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|89165100|gb|CI255157.1|CI255157
EST:     AGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: AGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88207178|gb|CI207027.1|CI207027
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88213746|gb|CI213595.1|CI213595
EST:     TCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: TCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88211494|gb|CI211134.1|CI211134
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88224604|gb|CI222784.1|CI222784
EST:     TCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: TCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|58589260|gb|CF987568.1|CF987568
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGACCAAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|29686974|gb|CB683249.1|CB683249
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|38480922|gb|CF965011.1|CF965011
EST:     GCACAGGTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGACCAAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|10930619|gb|AU160893.1|AU160893
EST:     ACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: ACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|33815301|gb|CF333502.1|CF333502
EST:     TCAGACGCGGGT-GTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: TCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88212873|gb|CI210724.1|CI210724
EST:     GTCTAATCAGACGCGGGTCTTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|11172025|gb|AU164079.1|AU164079
EST:     GCNCAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAG-ACACCAAGAAGA-GGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|33669977|gb|CF298216.1|CF298216
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCATTACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88208657|gb|CI208506.1|CI208506
EST:     GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: GCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
EST: gi|88211936|gb|CI211576.1|CI211576
EST:     AATCAGACGCGGGTCGTCAAGACTCCAG                         GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT
genomic: AATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGT

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), 75 (downstream exon)
Score: 126

GGCGGCGGCGGCGACGGCGAGATGGTGCAGCGCCTGACGTACCGCAAAAGGCACAGCTATGCCACGAAGTCTAATCAGACGCGGGTCGTCAAGACTCCAGgtctggatct ... gtggttgcagGTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA




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