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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcttagttttcgattgtacgacgtctgtgtcgctgactctagttttagtgttcaccatgaacaagagagcttgagctgtgaagcttggtagctgaataacttgtgttttctccaacactgctgggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT

Basic information

species Zea mays
transcript AC187157.4_FGT005
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g10320.1 (Oryza sativa), 3'ss of exon 9
gtaactcttagttttcgattgtacgacgtctgtgtcgctgactctagttttagtgttcaccatgaacaagagagcttgagctgtgaagcttggtagctgaataacttgtgttttctccaacactgctgggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT
                                 ||  ||  ||  | |  |     | | ||  |     |||  |     | |     ||     ||| | |||||||||| |   |   | |||     |||||||||||||| || ||||| |||| ||  ||||| || |||||||||||||||||||| || || |||||||||||||| || || || |||||||| || |
---------------------------------gtgactt-cttgattcatgagacttatcaccagttgaagaa-tcattttcttttttttttcctctgtaaaacttgtgttcttggcctgattgcaa---tggcagATGTACAATGGAGTAGAGGAGAGCAGTGCAGGAACATGTTCAGAGCTCATCTTTGCGCCCATCGACGCATCGTTCAGTGATGATTCCCCACTGCTGCCTT

upper sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g50679.1 (Oryza sativa), 3'ss of exon 9
gtaactcttagttttcgattgtacgacgtctgtgtcgctgactctagttttagtgttcaccatgaacaagagagcttgagctgtgaagcttggtagctgaataacttgtgttttctccaacactgctgggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT
                                 ||  ||  ||  | |  |     | | ||  |     |||  |     | |     ||     ||| | |||||||||| |   |   | |||     |||||||||||||| || ||||| |||| ||  ||||| || ||||||||||| |||||||| || || || ||||||||||| || || || || ||||| || |
---------------------------------gtgactt-cttgattcatgaaacttatcaccagttgaagaa-tcattttct----tttttcctctgtaaaacttgtgttcttggcctgattgcaa---tggcagATGTACAATGGAGTAGAGGAGAGCAGTGCAGGAACATGTTCAGAGCTAATCTTTGCACCCATCGATGCATCGTTCAGTGATGATTCTCCGCTGCTGCCTT
















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|22543133|gb|BU093571.1|BU093571
EST:     CCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAG                         ATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCCGAGCTCGTC
genomic: CCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATC
EST: gi|26457082|gb|CA828665.1|CA828665
EST:     CCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAG                         ATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCCGAGCTCGTC
genomic: CCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 25

TTCCTCGAGGTTATAAAAGTAGGAAATGCCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

TTCCTCGAGGTTATAAAAGTAGGAAATGCCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

TTCCTCGAGGTTATAAAAGTAGGAAATGCCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 19

TTCCTCGAGGTTATAAAAGTAGGAAATGCCGGTAACTACCAAGACGCGCTCCTGCACCGTGATCTGTTTCTGTTGCAGgtaactctta ... gggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagcttggtagctgaataacttgtgttttctccaacactgctgggttggcagATGTACAACGGGGTAGACGAGAACATGGCAGGCACTTGTTCAGAGCTCATCTTTGCCCCTATAGACGCATCGTTCAGCGACGACTCGCCACTGCTCCCAT
                gaataac  putative branch site (score: 19)
                 aataactt  TA-rich tract