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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagattgcactgttcgcagcgtggagtttgaatatgggtatgaggatgggtaagctactagagatagcctaaatctgagtaaaatttctgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC

Basic information

species Zea mays
transcript GRMZM2G147335_T03
intron # 9
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|166597509|gb|EG269877.1|EG269877
EST:     TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAG                         ATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGG
genomic: TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGG
EST: gi|78092631|gb|DV521005.1|DV521005
EST:     TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAG                         ATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGG
genomic: TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGG
EST: gi|78092632|gb|DV521006.1|DV521006
EST:     TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAG                         ATTAGTGGTGGTGCTGGTGAAGAACCAAATGGGNAACAAGCACTCACTAGG
genomic: TCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGG

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), 48 (downstream exon)
Score: 34

CAAACCGTCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 48

CAAACCGTCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

CAAACCGTCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

CAAACCGTCGATGCCAATGTAAATTTCAACGCACGGGAAGGAAGGAGTACCGTGGAGgtctgtaagc ... tgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgggtaagctactagagatagcctaaatctgagtaaaatttctgaaatgcagATTAGTGGTGGTGCTGGTGAAGAACCAAATGGAAAACAAGCACTCACTAGGTTTCAAAGGATTTGCACGGATGGGACTCACAGTATTGTCTTGTGCAAAC
                       gcctaaa  putative branch site (score: 26)
                                         tttct  putative PPT
                                    taaaatttctgaaat  TA-rich tract