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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTTGAAATCCATCTATTCTGGGCTGGAAAGGGCACTTGTTGTATTCCTATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaataattaagttaacataaaaatgattgcattggattccaataaatgaaatcctctttcag

Basic information

species Oryza sativa
transcript LOC_Os08g10310.2
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: AT1G56120.1 (Arabidopsis thaliana), 5'ss of exon 17
TTTCTTGAAATCCATCTATTCTGGGCTGGAAAGGGCACTTGTTGTATTCCTATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaataattaa---gttaacataaaaatgattg-cattggattccaataaatga-aatcctctttcag--------------
  ||| ||| ||||||| |||||||||||||| || || |||||||||||||| |||||    || || ||||| ||  | ||  | ||    || ||| ||||    ||   || |    ||    |     |||||  || |   | || |||   |  | | |  | |||               
CATCTCGAAGTCCATCTTTTCTGGGCTGGAAAAGGAACATGTTGTATTCCTATCCAAGGGGCTTATGGGCCATTAATAGCGGCCGTCAGTGCGACACCAGgtaacacaaacggttgatatattttttttcctctgattttcactatctcccgatactagttagtgccgtgtcacatattcttgttcag

upper sequence: LOC_Os08g10310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: AT1G56140.1 (Arabidopsis thaliana), 5'ss of exon 18
TTTCTTGAAATCCATCTATTCTGGGCTGGAAAGGGCACTTGTTGTATTCCTATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaataattaagttaacataaaaatgattgcattg-gattccaataaatgaaatcctctttcag------------
  ||| ||||| ||||| |||||||||||||| || || || ||||||||||| |||||    || || ||||| || || ||  |  |    || ||| ||||    |||  | || |   | |       |     |   ||| | | | | ||      | || ||             
CATCTCGAAATTCATCTTTTCTGGGCTGGAAAAGGAACATGCTGTATTCCTATCCAAGGGGCTTATGGGCCATTAATATCGGCCGTCGGTGCAACACCAGgtaaata-aatggtgaattcttcttgttttacaccatctcctgatgctagttagtgcttaagtgttacatatttctgttcag

upper sequence: LOC_Os08g10310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv00s0125g00140.t01 (Vitis vinifera), 5'ss of exon 5
TTTCTTGAAATCCATCTATTCTGGGCTGGAAAGGGCACTTGTTGTATTCCTATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaa-gcgtaataattaagttaacataaaaatgattgcatt---ggattccaataaatgaaa-tcctctttcag--------------------------------------
| ||||||||||||||| || |||||||| || || || || ||||||||| | ||||||||||| |||||||  || || ||  | |   |    ||| |||| ||     ||| | | |  ||| |   | |||  ||      | |    | |||||   |||| |||                                         
TATCTTGAAATCCATCTGTTTTGGGCTGGTAAAGGGACCTGCTGTATTCCTGTCCAAGGTTACTATGGACCATCCATTTCGGCCCTTACGGTTGTACCAGgtaatgcacttgaatgatggtt-catcattttcatttaatgtaaaaacttttctgaatgatgctcctgttttcttatcatggctgacaactgggtaccgttatttggttaag

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|33801536|gb|CF326640.1|CF326640
EST:     TATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTAGTCCTACTGTGCGAAACGGTGTACCCAAAAAGAAAAGTAAAGC
genomic: TATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaa ... cctctttcagATTTTAGTCCTACTGTGCGAAACGGTGTACCCAAAAAGAAAAGTAAAGC
EST: gi|569610|gb|D40459.1|D40459
EST:     CATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTAGTCCTACTGTGCGAAACGGTGTACCCAAAAAGAAAAGTAAAGCAG
genomic: CATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaa ... cctctttcagATTTTAGTCCTACTGTGCGAAACGGTGTACCCAAAAAGAAAAGTAAAGCAG
EST: gi|58607414|gb|CK035447.1|CK035447
EST:     TATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTAGTCCTACTGTGCGAAACGG
genomic: TATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaa ... cctctttcagATTTTAGTCCTACTGTGCGAAACGG

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: 53 (upstream exon), 48 (downstream exon)
Score: 4

TTTCTTGAAATCCATCTATTCTGGGCTGGAAAGGGCACTTGTTGTATTCCTATTCAAGGTTACTACGGACCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcgtaa ... cctctttcagATTTTAGTCCTACTGTGCGAAACGGTGTACCCAAAAAGAAAAGTAAAGCAGGTGCAATTGTTGGGATTGTGATTGCTGCCTCGGTTTTAGGATCAGCTAT




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