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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaaccttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTA

Basic information

species Oryza sativa
transcript LOC_Os06g24704.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 9
gttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaacctt-ttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTA
    || |  || || |  |||||   |  |||| |  |||||||  ||  ||  | |     || |||| |||||||||| || ||||||||||||| ||||||||||||||||||   ||| ||| |||| | || ||||||||||||||||| ||||||||||| |||||  |  |||||||||
---gttattgttgttttcagtcatgcatccattt-tatcaaaggtgcttcgtgtgtgg-----ttgtaacaatttaaccttgtttagGTAAGCAAAGCGCTTTATGCTGAATTTTTGGGTGCACAAAAGAAGCAGCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTA
















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|29670183|gb|CB666458.1|CB666458
EST:     TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG                         GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST: gi|29670228|gb|CB666503.1|CB666503
EST:     TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG                         GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST: gi|14571492|gb|BI118860.1|BI118860
EST:     TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG                         GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST: gi|29665965|gb|CB662240.1|CB662240
EST:     TTGATGTCCAGACTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG                         GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA

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: 58 (upstream exon), 58 (downstream exon)
Score: 21

TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcccaaaggtattttatgcttagattaattttaactatttaaccttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTA
                                              ccttttc  CT-rich tract
             tattttatgcttagat  TA-rich tract