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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatgagcagcacatatatataaatatggcaacacattgatcctctgtggcttatactttactatgaagtgtgaactcttcaactattttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG

Basic information

species Oryza sativa
transcript LOC_Os05g50970.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G158818_T01 (Zea mays), 3'ss of exon 5
gtaacatgagcagcacatatatataaatatggcaacacattgatcctctgtggcttatactttactatgaagtgtgaactcttcaactatttta---tcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
||||  ||| |  ||| |   | |||   ||      ||| | |  | |||   || |     | | | | |  | | || || |  | ||||    |||||||||||||||| ||||||| ||||||||||| ||| ||||||||||||||||||||||||||||||||||||||
gtaatttgatctacacct---tctaatgctgatgtttcatggcttatatgtaatttgtggc--attgt-aggcctaatctgtttacattttttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG

upper sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 7
gtaacatgagcagcacatatatataaatatggcaacacattgatcctctgtggcttatactttactatgaagtgtgaactcttcaactatttt-------atcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
||||  ||| | |||| |   | ||||||  |         |    | | ||  || |  ||  |  || ||    ||    | |||  ||||        |||||||||||||||| |||| || ||||||||||| ||| ||||||||||||||||||||||||||||| ||||||||
gtaagttgacctgcacgttattgtaaatactgatgtttcacggctttatatgtatttt-tttggcattgtagacctaatctgttaacatttttttttttggtcagGAACAAGAAATAAATGAGGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTTCGAATGAG
















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|89163537|gb|CI100427.1|CI100427
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|88969110|gb|CI099061.1|CI099061
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|89181946|gb|CI113452.1|CI113452
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|25807722|gb|CA763683.1|CA763683
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|86259723|gb|CI065596.1|CI065596
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|58687048|gb|CK075735.1|CK075735
EST:     TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: TTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
EST: gi|12623064|gb|AU173277.1|AU173277
EST:     AGATCCTGAGATTCAG                         GAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG
genomic: AGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGG

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: 65 (upstream exon), 58 (downstream exon)
Score: 33

GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAGgtaacatgag ... attttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctgtggcttatactttactatgaagtgtgaactcttcaactattttatcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
                                           ctatttt  CT-rich tract
           ttatactttactat  TA-rich tract