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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatgatgacaaagtttacttactggccattaacattttttttcacgtgaagctgttttatgacatctgcacgcattttgacttgcctcaattgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGGACTAGGTTTGACAGACAAGTCGCCAAATTCATGGGACATCTATGATCCA

Basic information

species Oryza sativa
transcript LOC_Os02g02350.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02350.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020366_T01 (Zea mays), 3'ss of exon 2
gtaaatatgatgacaaagtttacttactggccattaacattttttttcacgtgaagctgttt-tatgacatctgc--acgcattttgacttgcctcaa----ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGGACTAGGTTTGACAGACAAGTCGCCAAATTCATGGGACATCTATGATCCA
            |||     ||  |  | ||   | | |||  |  | | |  |  |  | | ||  | ||||      ||| ||     |||  |      ||  |||||||||||||||||| |||||| | ||  |  ||||  | ||||| |||| ||||   || ||||| |||||||| ||||||||||||||||||||||| || 
-----------aacagcacatatatg-tagcatgtcatattcgtccttaggcaacaccttatatactatatctattggagcagttccttatgctccgccgccttcctttcagGTGCTATTTTGTGTCTGCATCCCTTAAGGAGAAGTTGTACATAACTGATGGATACGGCTTGACGGACAAGTCACCAAATTCATGGGACATCTATGACCCG
















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|58667499|gb|CK056185.1|CK056185
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
EST: gi|218500348|gb|FG955858.1|FG955858
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
EST: gi|58685880|gb|CK074567.1|CK074567
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
EST: gi|29666903|gb|CB663178.1|CB663178
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
EST: gi|218495281|gb|FG959556.1|FG959556
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
EST: gi|33796083|gb|CF323908.1|CF323908
EST:     GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAG                         GTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG
genomic: GATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGG

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: 71 (upstream exon), 50 (downstream exon)
Score: 9

TGGGTGGTTGTAGCTGGCTAAAAGATGCTAATGATGAAGTATTTTGTTATGATGCCTCATCAAATTGCTGGAGCAGTGTAGCTCCAATGCCTACTGCTAGgtaaatatga ... ttgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGGACTAGGTTTGACAGACAAGTCGCCAAATTCATGGGACATCTATGATCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagctgttttatgacatctgcacgcattttgacttgcctcaattgttttcagGTGCTATTTTGTTTCTGCAGCTCTGGACAAGAAACTATACATTACTGGTGGACTAGGTTTGACAGACAAGTCGCCAAATTCATGGGACATCTATGATCCA
                             ttttgac  putative branch site (score: 9)
                                             ttgttttc  putative PPT
                                           aattgtttt  TA-rich tract