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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaacaacctttgtcaactactttcaaagctcgttggtgatctttaccttattacattcatttcagccacaaaccatttttcacaaattatggttgagcaacttattgcttgatatgctctgtaagtaatgcattatatggcaccgtgaagcatatcatcatttcatctattgcag

Basic information

species Oryza sativa
transcript LOC_Os05g28180.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 17
CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaacaacctttgtcaactactttcaaagctcgttggtgatcttt--accttattacattcatttcagccacaaac-catttttcacaaattatggttgagcaacttattgcttgatatgctctgtaagtaatgcattatatggcaccgtgaagcatatcatcatttcatctattgcag
|| |||||||||||||||||||||||||| ||||| || || |||||||| || ||||| |||||||||||||||||||||    || | | | ||||  | ||| || |  || | | || | | |  ||       |    | |       || | || | ||||| |    || ||    ||                                                                                
CTGTGGAAGCTCAGTTCTTGTGATTTATGCGAAATTGCGAGGAACTCTGTTTACCAATCTGGGTTTTCACATGCTCTCAAG-
















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|29675538|gb|CB671813.1|CB671813
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|29638453|gb|CB643462.1|CB643462
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|86481338|gb|CI123971.1|CI123971
EST:     CTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGCCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: CTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|29637475|gb|CB642484.1|CB642484
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
EST: gi|87022773|gb|CI269709.1|CI269709
EST:     AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAG                         GCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT
genomic: AAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGAT

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: 74 (upstream exon), 63 (downstream exon)
Score: 30

CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTCTATCAATCAGGGTTTTCACATGCTCTCAAGgcaagtaaac ... tctattgcagGCACACTGGATTGGCAAGAACTATTACAAAAGAGGACCTACAGGGAACGATATTCATAAAACTAATGTGCCTCACATCAGGGTTCAGTTTAGGGACTTG




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