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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgactgcattgcaacttagtgatcttagtcataaactcataatgatttcaataaaatccatagagctgtaaaattttcctatgtttattgaagaccttaatgaagtcctacgttggtctattggtggatgattttttattcaggttcaaatgctaactgctaagttcttttttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATGTCCATTTCCAAATCAAAGACCGTCACCTCTGATGATGAGAGTGAAACTG

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 20
splice site 3'
intron type U2

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|163927597|gb|EG709981.1|EG709981
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88491733|gb|CI429005.1|CI429005
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|29675208|gb|CB671483.1|CB671483
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|86600893|gb|CI356650.1|CI356650
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|12622483|gb|AU172696.1|AU172696
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTNTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|86436893|gb|CI118615.1|CI118615
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|25806037|gb|CA761998.1|CA761998
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|29630179|gb|CB635188.1|CB635188
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88507019|gb|CI434525.1|CI434525
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|29674001|gb|CB670276.1|CB670276
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|2428987|gb|C73450.1|C73450
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88258892|gb|CI359282.1|CI359282
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88247369|gb|CI247218.1|CI247218
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|86426423|gb|CI071520.1|CI071520
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|86430204|gb|CI082627.1|CI082627
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88502339|gb|CI429845.1|CI429845
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88512671|gb|CI440177.1|CI440177
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88503768|gb|CI431274.1|CI431274
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|86430421|gb|CI082844.1|CI082844
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88479417|gb|CI416688.1|CI416688
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
EST: gi|88504559|gb|CI432065.1|CI432065
EST:     CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG                         TTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG
genomic: CAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATG

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: 55 (upstream exon), 67 (downstream exon)
Score: 5

GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAGgtttgtgact ... tttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATGTCCATTTCCAAATCAAAGACCGTCACCTCTGATGATGAGAGTGAAACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgattttttattcaggttcaaatgctaactgctaagttcttttttctgacagTTATGTGCTACAAGTGGAAGTTCTCTGGGCTACGGATACTCGAGAGTCATGTCCATTTCCAAATCAAAGACCGTCACCTCTGATGATGAGAGTGAAACTG
                         tgctaac  putative branch site (score: 5)
                                       ttcttttttctgac  putative PPT
     attttttattca  TA-rich tract