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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgacaagttaggtcaatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os09g12550.1
intron # 13
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|86482193|gb|CI124826.1|CI124826
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|29627251|gb|CB632262.1|CB632262
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAAAACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|87014906|gb|CI271505.1|CI271505
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|66915004|gb|CX101852.1|CX101852
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAAGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCANGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|29673906|gb|CB670181.1|CB670181
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|58653118|gb|CK041798.1|CK041798
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA

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: 67 (upstream exon), 58 (downstream exon)
Score: 16

AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG
                              atctgat  putative branch site (score: 16)
               aatgaatatt  TA-rich tract