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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttactcctcagcaagttcatttaatctcctactatctatatttagtcctgagattgccttcatttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG

Basic information

species Zea mays
transcript GRMZM2G110309_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 4
gtaagattttactcctcagcaagttcatttaatctccta-ctatctatatttagt--------cctgagattgcct---tcatttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG
||||| |||  | ||     || |   ||| || |  ||  ||| |   |||  |         || ||| |||||   |   | |||||||| |||||||  || |||||||| |||||||||||||||||  |||| |||||||||| ||| |||||||| ||||| |||
gtaag-tttggccccatgaaaaatgtttttgatattgtaattattttggttttatggccatagtctaagactgcctgtttttctccttgcagTAAAACTTAGGATCAAGTCTTTCAAGGTGCCTGAACTTCTAATTGAGATCCCAGAAACTGCGACTGTTGGTTCACTGAAG
















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|32920498|gb|CF025310.1|CF025310
EST:     GACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG                         TGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|148942281|gb|EC887299.2|EC887299
EST:     GACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG                         TGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCC

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: 45 (upstream exon), 49 (downstream exon)
Score: 33

CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaatctcctactatctatatttagtcctgagattgccttcatttcttgcagTGAAACTTAAAATTAAGTCTTTTAAGGTGCCTGAACTTCTTGTTGAAATCCCAGAAAGTGCAACTGTTGGCTCACTAAAG
 atttaat  putative branch site (score: 160)
                                    ttgccttcatttctt  putative PPT
            tactatctatattta  TA-rich tract