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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtgatttgtcaaagatcttgctgcgtccgtttggactgcgtgtgtgtagagactattattgtgtgtgagacactgagactgacctggcgaaagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT

Basic information

species Zea mays
transcript GRMZM2G110714_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110714_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 11
gtgatgtgatttgtcaaagatcttgctgcgtccgtttggactgcgtgtgtgtagagactattattgtgtgtgagacactgagactgac---ctggcgaaagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT
        || |   ||  |   |        | | |  |   |  ||    |   |||  | || | | | |   |      |  ||   |||      |   |||||| ||||| ||||| |||||||||||||| || || ||| ||| |||||| ||||| |||||||| || |||| ||| |||||||| |||||||| || |
--------atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
















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|85151755|gb|DW587501.1|DW587501
EST:     GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAG                         GTCGCTGGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAG
genomic: GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGG-CACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAG
EST: gi|93015685|gb|EB641205.1|EB641205
EST:     GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAG                         GTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
genomic: GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
EST: gi|26457670|gb|CA829253.1|CA829253
EST:     GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAG                         GTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
genomic: GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
EST: gi|60347123|gb|DN214096.1|DN214096
EST:     GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAG                         GTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
genomic: GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
EST: gi|60353908|gb|DN220881.1|DN220881
EST:     GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAG                         GTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG
genomic: GGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGG

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), 44 (downstream exon)
Score: 146

CGCGGCGCTGTACGACAAGCTTCTGGTCTCAGAGGATCTGTGGGCATTAGGGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

CGCGGCGCTGTACGACAAGCTTCTGGTCTCAGAGGATCTGTGGGCATTAGGGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

CGCGGCGCTGTACGACAAGCTTCTGGTCTCAGAGGATCTGTGGGCATTAGGGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 104

CGCGGCGCTGTACGACAAGCTTCTGGTCTCAGAGGATCTGTGGGCATTAGGGGCGCGTCTCAGAGCCAACTACGAAGAAACAAAGCAGCTTCTCCTGCAGgtgatgtgat ... aagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagagactattattgtgtgtgagacactgagactgacctggcgaaagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT
                               gactgac  putative branch site (score: 104)
                                                ttttc  putative PPT
      actattatt  TA-rich tract