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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccctttacacaatgccagattttggcacattgccacagttgctagaaaatcatgtaatatttatgtacttgtacttacag

Basic information

species Oryza sativa
transcript LOC_Os10g30750.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g30750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
GTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagta-ccctttac-acaatgccagattttggcacattgccacagttgctagaaaatcatgtaatatttatgtacttgtacttacag
|| |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| |||||||||||| ||||  || | | | |||| | ||||||||||        | ||  ||||        || ||    || ||| ||| |||
GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagccctgcacgatacttccagctcttggcacatttgtttgcgtactgtaaaactg-actgtacttggtaacatgttcttgcag

upper sequence: LOC_Os10g30750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G06730.1 (Glycine max), 5'ss of exon 15
GTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccctttacaca-atgccagattttggcacattgccacagttgctagaaa--atcatgtaatatttatgtacttgtacttacag-----------------------------------------------------------------------------------------------
|||||||||||||| || || || ||||| ||  | || || |||||||||||||| || |||||| | || || || ||||||||||||||||     |  | |   ||  ||  | ||||     ||||    |  || |   |    || |  | |     |   |||     ||| |                                                                                                
GTTTGGAAGAAAGTGGTATATGTTGATAGACTACTCCAGCTCTTCAGATATGTACCCCGTGAACAATTGACCATCCCAGATTTTGTCTTTCAgttgagtctatgttttcatgtgttatatttataatcatttgttccttttcataatgctattacatgagtaacacacactctggtttaaatttattggaaattacaattaaataaaaagcgagacttagaagtaaatgtactttagattataggttctaattcattttgtacttttattctcaaag
















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|13165543|gb|AU174340.1|AU174340
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|29672652|gb|CB668927.1|CB668927
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|88456231|gb|CI544767.1|CI544767
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|58656780|gb|CK045460.1|CK045460
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|25803039|gb|CA759000.1|CA759000
EST:     TTCAGATATGTACCACGAGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|86828186|gb|CI276799.1|CI276799
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|86603018|gb|CI357382.1|CI357382
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAAC
EST: gi|89192107|gb|CI393464.1|CI393464
EST:     TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA                         GCATGAGTTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAA
genomic: TTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGA-TTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAA

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: 69 (upstream exon), 69 (downstream exon)
Score: 53

GTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagtaccc ... gtacttacagGCATGATTTGGAGGTGAACGGTGGGAGAGGCCTAATTGTTGACCCAAGAACAAAACACATTTATCAGAGACCGTCTGGCTGATGTAGATATTTCTGCGGT




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