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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttttacaaattggttatggctttggaacatatacatgtattgatagttcatgaaacaagtgttttccaacttgtcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT

Basic information

species Zea mays
transcript GRMZM2G065130_T01
intron # 5
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|211221898|gb|FL409207.1|FL409207
EST:     TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAG                         ATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA
genomic: TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA
EST: gi|74243504|gb|DT651418.1|DT651418
EST:     TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAG                         ATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA
genomic: TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA
EST: gi|211122374|gb|FL379873.1|FL379873
EST:     TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAG                         ATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA
genomic: TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAA

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), 48 (downstream exon)
Score: 177

TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 110

TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 84

TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 82

TACTCAGTGGAGATAACACCAAATAAAGCCAGTATACTTTCCAAGgttcgtttta ... tcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatacatgtattgatagttcatgaaacaagtgttttccaacttgtcctgtccagATCCTATCTGTTACAGTGAGGTCCATTCAGAAAGATGCTGAGGAAAAGAAAGCTTCATTTAATCCTCGACCATACTTCCGATTGTTTATAAATTGGCTCT
         tattgat  putative branch site (score: 82)
                                         cttgtcct  putative PPT
         tattgata  TA-rich tract