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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtttttgtcaagtcgcttctatattgttacatctgaattaacagaattgaaggagtaatttcagttatcattctttttaccttgtttgtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGGACACTACAATCCGTTTGTAGAGCCATAATTGCATTGATGGCCCATCCTG

Basic information

species Oryza sativa
transcript LOC_Os02g42314.1
intron # 4
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|2796274|gb|AA749568.1|AA749568
EST:     CGCAANT-CGCTTCTTGACCAAAATTTTGCGCCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCG
EST: gi|88334413|gb|CI642658.1|CI642658
EST:     GCAAGTTCGCTTCTTGACCAAAATTTTCCACCCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGGCTGGATATCTT
genomic: GCAAGTTCGCTTCTTGACCAAAATTTTCCACCC-GAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTT
EST: gi|9865085|gb|AU100835.1|AU100835
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTT
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTT
EST: gi|88386007|gb|CI570642.1|CI570642
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACACGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
EST: gi|88595265|gb|CI714086.1|CI714086
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCC
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCC
EST: gi|55438029|gb|CV732308.1|CV732308
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
EST: gi|88308370|gb|CI649585.1|CI649585
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCC
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCC
EST: gi|88342554|gb|CI637130.1|CI637130
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGG
EST: gi|86905439|gb|CI285402.1|CI285402
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
EST: gi|88393637|gb|CI619929.1|CI619929
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATT
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATT
EST: gi|88348941|gb|CI653985.1|CI653985
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCT
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCT
EST: gi|88595236|gb|CI714057.1|CI714057
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGC
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGC
EST: gi|33823074|gb|CF337340.1|CF337340
EST:     CGCAAGTTCGCT-CTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGA-TGCGTGGAGCCCAGCATGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGG
EST: gi|88592549|gb|CI710658.1|CI710658
EST:     CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAG                         ACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGG
genomic: CGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGG

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: 47 (upstream exon), 69 (downstream exon)
Score: 39

TGTATTTCAACTTGCATTCTCTATTCCTGAGCAATACCCTCTCCTTCCTCCGCAAGTTCGCTTCTTGACCAAAATTTTCCACCCGAATGTGCATTTCAAGgttacttctg ... gtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGGACACTACAATCCGTTTGTAGAGCCATAATTGCATTGATGGCCCATCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattgaaggagtaatttcagttatcattctttttaccttgtttgtgtttccagACAGGTGAGATTTGCCTGGATATCTTGAAGAATGCGTGGAGCCCAGCATGGACACTACAATCCGTTTGTAGAGCCATAATTGCATTGATGGCCCATCCTG
                                              tgtttcc  CT-rich tract
                      ttatcattcttttta  TA-rich tract