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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccaccttctcttaagcatctgaaatagtatatccctgaattaatacatttctgattgttagttagtctgaaattttgctgacagtgatttttttttgtttgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGTATAGGGAACCTCTCTACTCAGTATGCATGGGCATATGTAGGTCTCTCAG

Basic information

species Oryza sativa
transcript LOC_Os12g31850.4
intron # 2
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|88406805|gb|CI603999.1|CI603999
EST:     TCGGGGATAGCAAGCCCAAAATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88765956|gb|CI775046.1|CI775046
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTT
EST: gi|86888374|gb|CI303656.1|CI303656
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88736973|gb|CI760481.1|CI760481
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTG
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTG
EST: gi|87004914|gb|CI308790.1|CI308790
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88443662|gb|CI591887.1|CI591887
EST:     CGGCGATAGCAAGCCCAAAATGCACAATTTCTTCACCCAGCCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAG
genomic: CGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGC-TCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAG
EST: gi|86888306|gb|CI301998.1|CI301998
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|29614658|gb|CB619671.1|CB619671
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88315752|gb|CI617225.1|CI617225
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTG
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATT-GGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTG
EST: gi|86826073|gb|CI310964.1|CI310964
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88299367|gb|CI572319.1|CI572319
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|86888337|gb|CI303619.1|CI303619
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGCGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|87017707|gb|CI289840.1|CI289840
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGC
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGC
EST: gi|88372698|gb|CI612626.1|CI612626
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTTGCAATGGCAGGGGGTGTTGTTGCTCA
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTT-GCAATGGCAGGGGGTGTTGT-GCTCA
EST: gi|88826059|gb|CI776624.1|CI776624
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGG
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGG
EST: gi|29665274|gb|CB661549.1|CB661549
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|86909428|gb|CI304662.1|CI304662
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|86891687|gb|CI309971.1|CI309971
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|88308904|gb|CI654187.1|CI654187
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|29614656|gb|CB619669.1|CB619669
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
EST: gi|86905004|gb|CI289151.1|CI289151
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAA
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAA
EST: gi|86826242|gb|CI311080.1|CI311080
EST:     TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAG                         GATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT
genomic: TCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGT

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: 72 (upstream exon), 75 (downstream exon)
Score: 38

GATCACGAACCTCCTCGCTGCGGTCCTCATCGCGCTCACCTTCGGTCAGCTCGGCGATAGCAAGCCCAACATGCCCAATTTCTTCACCCAGCTCAGTCAGgttagccacc ... tgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGTATAGGGAACCTCTCTACTCAGTATGCATGGGCATATGTAGGTCTCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttagttagtctgaaattttgctgacagtgatttttttttgtttgcaatgaagGATAATTGGCCTTCAGTGCTGTTTGCAATGGCAGGGGGTGTTGTGCTCAGTATAGGGAACCTCTCTACTCAGTATGCATGGGCATATGTAGGTCTCTCAG
                     tgctgac  putative branch site (score: 38)
                                 tttttttttgtttgc  putative PPT
                              tgatttttttttgttt  TA-rich tract